Ion Exchange Chromatography PDF

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Chromatography
Principles and Methods
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Ion Exchange Chromatography

11000421 AC 1
Contents
Introduction.........................................................................................................................................7
Symbols ............................................................................................................................................................................... 8
Common acronyms and abbreviations ............................................................................................................... 8
Chapter 1
Principles of ion exchange ............................................................................................................. 11
Net surface charge and pH .....................................................................................................................................11
Steps in an IEX separation .......................................................................................................................................12
Equilibration.............................................................................................................................................................12
Sample application and wash ........................................................................................................................12
Elution .........................................................................................................................................................................12
Regeneration .........................................................................................................................................................12
Resolution .........................................................................................................................................................................14
Efficiency ...................................................................................................................................................................15
Selectivity..................................................................................................................................................................17
Components of IEX media ........................................................................................................................................21
Matrix ..........................................................................................................................................................................21
Functional groups.................................................................................................................................................23
Binding capacity and recovery ..............................................................................................................................24
Chromatofocusing........................................................................................................................................................25
Chapter 2
Ion exchange in practice ............................................................................................................... 27
Introduction .....................................................................................................................................................................27
Selecting chromatography media .......................................................................................................................27
Capture ......................................................................................................................................................................27
Intermediate purification ..................................................................................................................................27
Polishing ....................................................................................................................................................................27
Fast IEX media selection and method development ..........................................................................30
Practical considerations for IEX separation ....................................................................................................30
Buffer pH and ionic strength...........................................................................................................................30
Anion or cation exchanger ..............................................................................................................................31
Strong or weak ion exchangers .....................................................................................................................32
Buffer selection and preparation .................................................................................................................33
Flow rates .................................................................................................................................................................34
Flow control .............................................................................................................................................................35
Steps in an IEX separation ........................................................................................................................................36
Column and media preparation ....................................................................................................................36
Sample preparation.............................................................................................................................................37
Sample application and wash ........................................................................................................................37
Sample load .............................................................................................................................................................38
2 11000421 AC
Elution of target protein.....................................................................................................................................39

Linear gradient elution ......................................................................................................................................39
Step elution ..............................................................................................................................................................41
pH elution..................................................................................................................................................................42
Regeneration and re-equilibration ..............................................................................................................43
Detergents, denaturing agents, and other additives ................................................................................43
Analysis of results and further steps ..................................................................................................................45
Scaling-up ........................................................................................................................................................................45
Equipment selection....................................................................................................................................................46
Care of IEX media..........................................................................................................................................................46
Troubleshooting .............................................................................................................................................................47
Chapter 3
Ion exchange chromatography media........................................................................................ 53
Introduction .....................................................................................................................................................................53
MiniBeads: purification or analysis of microgram to milligram
quantities with high resolution .............................................................................................................................53
Media characteristics .........................................................................................................................................53
Purification options ..............................................................................................................................................54
Purification examples .........................................................................................................................................55
Performing a separation ...................................................................................................................................56
Cleaning.....................................................................................................................................................................57
Chemical stability .................................................................................................................................................58
Storage .......................................................................................................................................................................58
MonoBeads: purification of milligram quantities with high resolution .............................................59
Performing a separation ..................................................................................................................................63
Cleaning.....................................................................................................................................................................65
Storage .......................................................................................................................................................................65
SOURCE: high-throughput, high-resolution purification, and easy scale-up .................................66
Cleaning.....................................................................................................................................................................74
Storage .......................................................................................................................................................................74
11000421 AC 3
Sepharose High Performance: purification with high resolution .........................................................75

Cleaning ...................................................................................................................................................................80
Storage .......................................................................................................................................................................81
Sepharose Fast Flow: purification with good resolution and easy scale-up ..................................82
Cleaning.....................................................................................................................................................................89
Storage .......................................................................................................................................................................90
Sepharose XL: for selected proteins that require very high binding capacity
to increase productivity, easy scale-up .............................................................................................................91
Cleaning.....................................................................................................................................................................96
Storage .......................................................................................................................................................................97
Sepharose Big Beads: purification from crude, viscous samples at large scale .........................98
Performing a separation ................................................................................................................................ 100
Cleaning.................................................................................................................................................................. 100
Chemical stability .............................................................................................................................................. 101
Storage .................................................................................................................................................................... 101
Capto: high-flow media with high resolution ............................................................................................. 102
Media characteristics ...................................................................................................................................... 102
Purification options ........................................................................................................................................... 103
Purification examples ...................................................................................................................................... 105
Intermediate purification of insulin........................................................................................................... 106
Polishing of MAb ................................................................................................................................................. 107
Chapter 4
Ion exchange in a Purification Strategy (Cipp) ........................................................................ 111
Applying Cipp ............................................................................................................................................................... 111
Selection and combination of purification techniques........................................................................... 112
Ion exchange as a capture step ......................................................................................................................... 115
Capture using Sepharose Q XL .......................................................................................................................... 116
Ion exchange for intermediate purification.................................................................................................. 117
Ion exchange as a polishing step ...................................................................................................................... 119
Alternative techniques for polishing ................................................................................................................ 120
4 11000421 AC
Chapter 5
Large-scale purification .............................................................................................................. 121
BioProcess media for IEX ....................................................................................................................................... 121
Capture purification.......................................................................................................................................... 122
Polishing purification ....................................................................................................................................... 123
Prepacked, disposable solutions speed up the downstream process............................................ 127
Custom Designed Media ....................................................................................................................................... 127
Appendix 1
Sample preparation ...................................................................................................................... 129
Sample stability .......................................................................................................................................................... 129
Sample clarification .................................................................................................................................................. 129
Centrifugation ..................................................................................................................................................... 130
Filtration ................................................................................................................................................................. 130
Desalting ............................................................................................................................................................... 131
Specific sample preparation steps ................................................................................................................... 131
Fractional precipitation .................................................................................................................................. 131
Ammonium sulfate precipitation ............................................................................................................... 132
Resolubilization of protein precipitates ..................................................................................................134
Buffer exchange and desalting ..........................................................................................................................134
Removal of lipoproteins .......................................................................................................................................... 136
Removal of phenol red ............................................................................................................................................ 136
Removal of low molecular weight contaminants ...................................................................................... 136
Appendix 2
Nonvolatile and volatile buffer systems................................................................................... 137
Nonvolatile buffers for anion exchange chromatography ................................................................... 137
Nonvolatile buffers for cation exchange chromatography.................................................................. 138
Volatile buffer systems ........................................................................................................................................... 138
Appendix 3
Column packing and preparation ............................................................................................. 139
Column selection ........................................................................................................................................................141
Column packing and efficiency ...........................................................................................................................141
Appendix 4
Selection of purification equipment .......................................................................................... 143
Appendix 5
Converting from flow velocity to volumetric flow rates ....................................................... 145
From flow velocity (cm/h) to volumetric flow rate (ml/min) ................................................................. 145
From volumetric flow rate (ml/min) to flow velocity (cm/h)................................................................... 145
From volumetric flow rate (ml/min) to using a syringe ........................................................................... 146
11000421 AC 5
Appendix 6
Conversion data: Conversion data: proteins, column pressures ........................................ 147
Proteins ............................................................................................................................................................................147
Column pressures .......................................................................................................................................................147
Appendix 7
Table of amino acids ..................................................................................................................... 148
Appendix 8
Analytical assays during purification ....................................................................................... 150
Total protein determination .................................................................................................................................. 150
Purity determination ................................................................................................................................................ 150
Functional assays ...................................................................................................................................................... 151
Detection and assay of tagged proteins........................................................................................................ 152
Appendix 9
Storage of biological samples..................................................................................................... 153
General recommendations ................................................................................................................................... 153
Specific recommendations for purified proteins........................................................................................ 153
Appendix 10
Column cleaning ............................................................................................................................ 154
Removing precipitated proteins, lipids, hydrophobically bound proteins, or lipoproteins ....154
To remove precipitated proteins ................................................................................................................154
To remove lipids, hydrophobically bound proteins, or lipoproteins ..........................................154
Extended cleaning procedures ........................................................................................................................... 155
Appendix 11
Media selection.............................................................................................................................. 156
Selection of media for automated purification .......................................................................................... 156
Selection of media for manual purification .................................................................................................. 157
Using PD-10 columns for media selection and method development .......................................... 158
Related literature .......................................................................................................................... 160
Ordering information ................................................................................................................... 161
Acessories and spare parts......................................................................................................... 165
Product index ................................................................................................................................. 166
6 11000421 AC
Introduction
Biomolecules are purified using chromatography techniques that separate them according to
differences in their specific properties, as shown in Figure I.1. Ion exchange chromatography
(IEX) separates biomolecules according to differences in their net surface charge.
Property
Technique
Charge
Ion exchange chromatography (IEX)
Size
Size exclusion chromatography (SEC), also called gel filtration (GF)
Hydrophobicity
Hydrophobic interaction chromatography (HIC)

Reversed phase chromatography (RPC)
Biorecognition (ligand specificity)
Affinity chromatography (AC)
Size exclusion
Hydrophobic
interaction
Ion exchange
Affinity
Reversed phase
Fig I.1. Separation principles in chromatographic purification.
IEX for the separation of biomolecules was introduced in the 1960s and continues to play
a major role in the separation and purification of biomolecules. Today, IEX is one of the most
frequently used techniques for purification of proteins, peptides, nucleic acids, and other
charged biomolecules, offering high resolution and group separations with high loading capacity.
The technique is capable of separating molecular species that have only minor differences
in their charge properties, for example two proteins differing by one charged amino acid.
These features make IEX well suited for capture, intermediate purification, or polishing steps
in a purification protocol and the technique is used from microscale purification and analysis
through to purification of kilograms of product.
This handbook describes both theoretical and practical aspects principles of the technique,
the chromatography media (resins) available and how to select them, application examples,
and detailed instructions for the most commonly performed procedures. Practical information,
with many tips and hints drawn from over 50 yr of experience in chromatography purification,
guides beginners and experts towards obtaining optimal results from the latest
chromatography media.
GE Healthcares Life Sciences business offers a wide variety of prepacked columns and
ready-to-use chromatography media. A range of handbooks ensure that purification with
any chromatographic technique becomes a simple and efficient procedure at most scales
and in most laboratories.
11000421 AC 7
Symbols
This symbol indicates general advice on how to improve procedures or recommends
measures to take in specific situations
This symbol indicates where special care should be taken
Highlights chemicals, buffers, and equipment
Outline of experimental protocol
Common acronyms and abbreviations

A280
UV absorbance at specified wavelength (in this example, 280 nm)
AC
affinity chromatography
AIEX
anion exchange chromatography
APMSF
4-aminophenyl-methylsulfonyl fluoride
AU
absorbance units
BSA
bovine serum albumin
cGMP
current good manufacturing practice
CF
chromatofocusing
CHO
Chinese hamster ovary
CIEX
cation exchange chromatography
CIP
cleaning-in-place
CIPP
capture, intermediate purification, polishing
CV
column volume
Dab
domain antibody, the smallest functional entity of an antibody
DNA
deoxyribonucleic acid
DNAse
deoxyribonuclease
DOC
deoxycholate
DoE
design of experiments
DS
desalting (group separation by size exclusion chromatography;

buffer exchange)
EDTA
ethylene diaminetetraacetic acid
EGTA
ethylene glycol-O,O-bis-[2-amino-ethyl]-N,N,N,N,-tetraacetic acid
ELISA
enzyme-linked immunosorbent assay
F(ab)2 fragment
fragment with two antigen binding sites, obtained by pepsin digestion
Fab fragment
antigen binding fragment obtained by papain digestion
Fc fragment
crystallizable fragment obtained by papain digestion
Fv fragment
unstable fragment containing the antigen binding domain
GF
gel filtration; also called size exclusion chromatography
GST
glutathione S-transferase
8 11000421 AC
HCP
host cell protein
HIC
hydrophobic interaction chromatography
HMW
high molecular weight
HSA
human serum albumin
IEX
ion exchange chromatography
IgA, IgG etc.
different classes of immunoglobulin
IMAC
Immobilized metal ion affinity chromatography
LC-MS
liquid chromatographymass spectrometry
LMW
low molecular weight
MAb
monoclonal antibody
MPa
megaPascal
Mr
relative molecular weight
MS
mass spectrometry
native, as in nProtein A
NC
nitrocellulose
NHS
N-hydroxysuccinimide
PAGE
polyacrylamide gel electrophoresis
PBS
phosphate buffered saline
PEG
polyethylene glycol
pI
isoelectric point, the pH at which a protein has zero net surface charge
PMSF
phenylmethylsulfonyl fluoride
psi
pounds per square inch
PVDF
polyvinylidene fluoride
PVP
polyvinylpyrrolidine
recombinant, as in rProtein A
RNA
ribonucleic acid
RNAse
ribonuclease
RPC
reversed phase chromatography
scFv
single chain Fv fragment
SDS
sodium dodecyl sulfate
SDS-PAGE
sodium dodecyl sulfate polyacrylamide gel electrophoresis
SEC
size exclusion chromatography
TCEP
tris(2-carboxyethyl) phosphine hydrochloride
TFA
Trifluoroacetic acid
Tris
tris-(hydroxymethyl)-aminomethane
UV
ultraviolet
v/v
volume to volume
w/v
weight to volume
11000421 AC 9
10 11000421 AC
Chapter 1
Principles of ion exchange
This chapter provides a general introduction to the theoretical principles that underlie every ion
exchange separation. An understanding of these principles will enable the separation power of
ion exchange chromatography (IEX) to be fully appreciated. Practical aspects of performing a
separation are covered in Chapter 2.
Net surface charge and pH

IEX separates molecules on the basis of differences in their net surface charge. Molecules vary
considerably in their charge properties and will exhibit different degrees of interaction with
charged chromatography media according to differences in their overall charge, charge density,
and surface charge distribution. The charged groups within a molecule that contribute to the net
surface charge possess different pKa values (acid ionization constant) depending on their
structure and chemical microenvironment.
Since all molecules with ionizable groups can be titrated, their net surface charge is highly pH
dependent. In the case of proteins, which are built up of many different amino acids containing
weak acidic and basic groups, net surface charge will change gradually as the pH of the
environment changes, that is, proteins are amphoteric. Each protein has its own unique net
charge versus pH relationship which can be visualized as a titration curve. This curve reflects
how the overall net charge of the protein changes according to the pH of the surroundings.
Figure 1.1 illustrates several theoretical protein titration curves (these curves can be generated
using a combination of isoelectric focusing and electrophoresis, but with modern solutions for
rapid method development, actual titration curves are rarely used).
+
Surfac e net charge
Cation
pH
Anion
Fig 1.1. Theoretical protein titration curves, showing how net surface charge varies with pH.
IEX takes advantage of the fact that the relationship between net surface charge and pH is
unique for a specific protein. In an IEX separation, reversible interactions between charged
molecules and oppositely charged IEX media are controlled in order to favor binding or elution
of specific molecules and achieve separation. A protein that has no net charge at a pH equivalent
to its isoelectric point (pI) will not interact with a charged medium. However, at a pH above its
pl, a protein will bind to a positively charged medium or anion exchanger and, at a pH below its
pI, a protein will bind to a negatively charged medium or cation exchanger. In addition to the
ion-exchange interaction, other types of binding can occur, but these effects are very small
and mainly due to van der Waals forces and nonpolar interactions.
11000421 AC 11
Steps in an IEX separation

An IEX medium comprises a matrix of spherical particles substituted with ionic groups that are
negatively or positively charged. The matrix is usually porous to give a high internal surface
area. The medium is packed into a column to form a packed bed. The bed is then equilibrated
with buffer which fills the pores of the matrix and the space in between the particles.
Equilibration
The first step is the equilibration of the stationary phase to the desired start conditions. When
equilibrium is reached, all stationary phase charged groups are bound with exchangeable
counterions, such as chloride or sodium. The pH and ionic strength of the start buffer are
selected to ensure that, when sample is loaded, proteins of interest bind to the medium and as
many impurities as possible do not bind.
Sample application and wash

The second step is sample application and wash. The goal in this step is to bind the target
molecule(s) and wash out all unbound material. The sample buffer should have the same pH
and ionic strength as the start buffer in order to bind all charged target proteins. Oppositely
charged proteins bind to ionic groups of the IEX medium, becoming concentrated on the
column. Uncharged proteins, or those with the same charge as the ionic group, pass through
the column at the same speed as the flow of buffer, eluting during or just after sample
application, depending on the total volume of sample loaded.
Elution
When all the sample has been loaded and the column washed with start buffer so that all
nonbinding proteins have passed through the column, conditions are altered in order to elute
the bound proteins. Most frequently, proteins are eluted by increasing the ionic strength (salt
concentration) of the buffer or, occasionally, by changing the pH. As ionic strength increases
the salt ions (typically Na+ or Cl-) compete with the bound components for charges on the
surface of the medium and one or more of the bound species begin to elute and move down
the column. The proteins with the lowest net charge at the selected pH will be the first ones
eluted from the column as ionic strength increases. Similarly, the proteins with the highest
charge at a certain pH will be most strongly retained and will be eluted last. The higher the net
charge of the protein, the higher the ionic strength that is needed for elution. By controlling
changes in ionic strength using different forms of gradient, proteins are eluted differently in a
purified, concentrated form.
Regeneration
A final wash with high ionic strength buffer regenerates the column and removes any
molecules still bound. This ensures that the full capacity of the stationary phase is available for
the next run. The column is then re-equilibrated in start buffer before starting the next run.
The above describes a typical IEX separation. Alternatively, conditions can be chosen to
maximize the binding of contaminants to allow the target protein(s) to first pass through the
column to be collected.
12 11000421 AC
Positively
charged
ionic groups
Low ionic
strength
buffer
Absorption
Equilibration
Matrix
IEX medium equilibrated with

start buffer.
Time/Volume
Negatively
charged
proteins
Absorption
Neutral or
positively
charged
proteins
Time/Volume
Oppositely charged proteins

bind to ionic groups of the
IEX medium, becoming concentrated on the column. Uncharged proteins, or those with
the same charge as the ionic
groups, elute during sample
application or just after, during
the wash with start buffer.
Absorption
Elution 1
Increasing ionic strength

(using a gradient) displaces
bound proteins as ions in the
buffer compete for binding sites.
Time/Volume
Elution 2
Absorption
Further increases in ionic

strength displace proteins that
are more highly charged (more
tightly bound)
Time/Volume
Absorption
Elution 3
Time/Volume
Absorption
Regeneration
Final high ionic strength wash

removes any ionically bound
proteins before re-equilibration
Time/Volume
Fig 1.2. Principles of an anion exchange separation.

11000421 AC 13
Resolution
The resolution of an IEX separation is a combination of the degree of separation between
the peaks eluted from the column (the selectivity of the medium), the ability of the column to
produce narrow, symmetrical peaks (efficiency) and, of course, the amount (mass) of sample
applied. These factors are influenced by practical issues such as matrix properties, binding and
elution conditions, column packing, and flow rates which are covered in detail in Chapter 2,
Ion exchange in practice.
UV
Resolution (Rs ) is defined as the distance between peak maxima compared with the average
base width of the two peaks. Rs can be determined from a chromatogram, as shown in Figure 1.3.
Rs =
VR1
VR2
wb1
wb2
2 ( VR2 VR1 )
wb1 + wb2
Volume
Fig 1.3. Determination of the resolution (Rs) between two peaks.
Elution volumes and peak widths are measured with the same units to give a dimensionless
resolution value. Rs gives a measure of the relative separation between two peaks and can be
used to determine if further optimization of the chromatographic procedure is necessary.
If Rs = 1.0 (Fig 1.4) then 98% purity has been achieved at 98% of peak recovery, provided the
peaks are symmetrical and approximately equal in size. Baseline resolution requires that
Rs 1.5. At this value, peak purity is 100%.
A
UV
UV
R s = 1.5
R s = 1.0
98% A
2% B
98% B
2% A
Volume
Volume
~100% A
~100% B
Fig 1.4. Separation results with different resolutions.
A single, well-resolved peak is not necessarily a pure substance, but might represent a
series of components that could not be separated under the chosen elution conditions.
14 11000421 AC
Efficiency
Column efficiency (the ability to elute narrow, symmetrical peaks from a packed bed) relates to the
zone broadening which occurs on the column and is frequently stated in terms of the number
of theoretical plates (see Appendix 3 for determination of column efficiency). One of the main
causes of zone broadening is longitudinal diffusion of the solute molecules, that is, proteins,
peptides, or oligonucleotides. Zone broadening can be minimized if the distances available
for diffusion are minimized. In all situations, a well-packed column will contribute significantly
to resolution. Columns that are packed unevenly, too tightly, too loosely, or that contain
air bubbles will lead to channeling (uneven passage of buffer through the column), zone
broadening and hence loss of resolution. Figure 1.5 illustrates the parameters that contribute
to good column efficiency. Obviously particle size is a significant factor in resolution and, in
general, the smallest particles will produce the narrowest peaks under the correct elution
conditions and in a well-packed column.
Rapid exchange of counterions, typically Na+ or Cl-, and
solute molecules
Buffer flow
Rapid diffusion
Small bead size

Uniform pore size distribution
Even buffer flow distribution

Uniform packing
Narrow particle size distribution
Narrow, symmetrical peaks

Minimal zone broadening
Fig 1.5. Factors that affect column efficiency.
11000421 AC 15
Figure 1.6 demonstrates the influence of particle size on efficiency by comparing several
different IEX media under exactly the same running conditions. Note that different media
selectivities also influence the final resolution.
A 280
Mini Q
(column 4.6 50 mm)
3 m
Sample: Pancreatin
Gradient elution
5.0
10.0
ml
15. 0
A 280
Mono Q
(column 5 50 mm)
10 m
Sample: Pancreatin
Gradient elution
10
min
20
30
A 280
RESOURCE Q, 1 ml
Sample: Pancreatin
Gradient elution
15 m
Partic le siz e in c re as es
10
min
20
30
A 280
SOURCE 30Q
(XK16 50 mm)
30 m
Sample: Pancreatin
Gradient elution
0
10
min
20
30
A 280
Q Sepharose High Performance

(XK16 50 mm)
34 m
Sample: Pancreatin
Gradient elution
0
10
min
20
30
A 280
Q Sepharose Fast Flow

(XK16 50 mm)
90 m
Sample: Pancreatin
Gradient elution
0
10
min
20
30
Fig 1.6. Examples of the influence of particle size and selectivity on final resolution.
16 11000421 AC
R e solu tion in c re ase s
Although resolution in terms of efficiency can be improved by decreasing the particle

size of the matrix, using a smaller particle size often creates an increase in back
pressure so that flow rates need to be decreased, lengthening the run time. Hence the
need to match the medium with the requirements for the purification (speed, resolution,
recovery, and capacity).
The viscosity of highly concentrated samples might reduce resolution if large sample
volumes are loaded onto columns packed with small particles. Samples may be diluted
or, alternatively, a larger particle size should be used.
Selectivity
Good selectivity (the degree of separation between peaks) is a more important factor than
high efficiency in determining resolution (Fig 1.7) and depends not only on the nature
and number of the functional groups on the matrix, but also on the experimental conditions,
such as pH (influencing the protein charge), ionic strength, and elution conditions. It is the
ease and predictability with which these experimental conditions can be manipulated, when
using a suitably designed chromatography medium, that gives IEX the potential of extremely
high resolution.
Good selectivity
Bad selectivity
high efficiency
UV
UV
high efficiency
low efficiency
low efficiency
Fig 1.7. Effect of selectivity and efficiency on resolution.
Selectivity and pH
Good selectivity is achieved by performing IEX separations at pH values carefully selected to
maximize the differences in net charge of the components of interest. Figure 1.8 emphasizes
the significance of pH.
Optimum selectivity can be expected at a pH where there is maximum separation between
the titration curves for the individual proteins (i.e., the difference in net charges between the
species is greatest) and when using an ion exchanger with a charge opposite to the charge of
the proteins at the particular pH.
The order in which proteins are eluted cannot always be predicted with absolute certainty
since a titration curve (produced in practice by measuring electrophoretic mobility in a gel)
reflects the total net charge on a protein and IEX depends on the net charge on the surface of
the protein.
11000421 AC 17
Most alkaline pH: all three proteins are

above their pI, negatively charged, and
bind only to the anion exchanger. Proteins
are eluted in the order of their net charge.
Most acidic pH: all three proteins are below

their pI, positively charged, and bind only to
a cation exchanger. Proteins are eluted in
the order of their net charge.
Abs
Abs
Abs
Abs
Surface net charge
Cation
pH
Anion
Abs
Abs
Abs
Abs
Less acidic pH: blue protein is above its pI,

negatively charged, other proteins are still
positively charged. Blue protein binds to
an anion exchanger and can be separated
from the other proteins which wash through.
Alternatively, red and green proteins can be
separated on a cation exchanger and the blue
protein washes through.
Fig 1.8. Effect of pH on protein binding and elution patterns.
18 11000421 AC
Less alkali pH: red protein below its pI,

positively charged. Red protein binds to
cation exchanger and can be separated
from the other proteins which wash
through. Alternatively, blue and green
proteins can be separated on an anion
exchanger and the red protein washes
through.
Selectivity and elution

The figures below illustrate the most common forms of IEX separation in which proteins are
eluted by increasing the ionic strength of a buffer (typically with NaCl) using linear gradient or
step elution. The UV absorbance and conductivity traces show the elution of protein peaks and
the changes in salt concentration, respectively, during elution.
Buffer volumes used during sample application, elution, washing and re-equilibration
are expressed in column volumes (CV), for example 5 CV = 5 ml for a column with a 1 ml
bed volume. Using CV to describe a separation profile facilitates method development
and transfer of methods to columns of different dimensions when scaling-up.
Gradient elution (Fig 1.9) is often used when starting with an unknown sample (as many
components as possible are bound to the column and eluted differentially to see a total protein
profile) and for high-resolution separation or analysis.
equilibration
sample
injection
volume
gradient
elution
regeneration
1M
NaCl concentration
re-equilibration
high salt wash

5 CV
unbound molecules elute

before gradient begins
tightly bound
molecules
elute in high
salt wash
10 to 20 CV
5 to 10 CV
5 to 10 CV
Column volumes (CV)
Fig 1.9. Typical high-resolution IEX separation using linear gradient elution.
Step elution is used in several ways. When an IEX separation has been optimized using gradient
elution, changing to a step elution speeds up separation times and reduces buffer consumption
while retaining the required purity level (Fig 1.10).
high salt wash
NaCl concentration
1M
sample
injection
volume
unbound
molecules
elute
elution of
unwanted
material
5 CV
elution
of target
molecule
5 CV
tightly bound
molecules
elute
5 CV
equilibration
re-equilibration
5 to 10 CV
0
5 to 10 CV
Column volumes (CV)
Fig 1.10. Typical IEX separation using step elution.
11000421 AC 19
Step elution can also be used for group separation in order to concentrate the proteins of interest
and rapidly remove them from unwanted substances (Fig 1.11). The target protein(s) is eluted in
an enriched, concentrated form.
high salt wash
5 to 10 CV
NaCl concentration
1M
sample
injection
volume
unbound
molecules
elute
elution of
target
molecules
5 CV
equilibration
5 to 10 CV
0
re-equilibration
5 to 10 CV
Column volumes (CV)
Fig 1.11. Typical IEX separation using a step elution to separate groups of proteins with very different
charge properties.
Occasionally, step elution is used to remove contaminants by choosing conditions that

maximize binding of the contaminants and allow the target protein(s) to pass through the
column (Fig 1.12). Care must be taken to ensure that the binding capacity of the column is
sufficient to bind all contaminants.
high salt wash elutes
contaminants, 5 to 10 CV
NaCl concentration
1M
sample
injection
volume
target molecules
elute in wash
re-equilibration
5 to 10 CV
equilibration
5 to 10 CV
0
Column volumes (CV)
Fig 1.12. Contaminant removal: target protein(s) elute in the wash, contaminants bind to the column.
20 11000421 AC
Components of IEX media

Chromatography media for ion exchange are made from porous or nonporous matrices,
chosen for their physical stability, their chemical resistance to stringent cleaning conditions,
and their low level of nonspecific interaction. The matrices are substituted with functional
groups that determine the charge of the medium.
Matrix
High porosity offers a large surface area covered by charged groups and so ensures a high
binding capacity. High porosity is also an advantage when separating large biomolecules.
Nonporous matrices are preferable for extremely high-resolution separations when
diffusion effects must be avoided.
An inert matrix minimizes nonspecific interactions with sample components.
High physical stability ensures that the volume of the packed medium remains constant
despite extreme changes in salt concentration or pH thus improving reproducibility and
avoiding the need to repack columns.
High physical stability and uniformity of particle size facilitate high flow rates, particularly
during cleaning or re-equilibration steps, to improve throughput and productivity.
High chemical stability ensures that the matrix can be cleaned using stringent cleaning
solutions if required.
Modern IEX media use either polymer or agarose-based matrices to fulfil not only the
requirements for high binding capacity, chemical and physical stability, but to generate
media with suitable particle sizes for a range of applications (Table 1.1).
Table 1.1. Ion exchange matrices
Form
Mean particle size (m)
MiniBeads
Polystyrene/divinyl benzene
MonoBeads
10
SOURCE 15
15
SOURCE 30
30
Sepharose High Performance
Agarose 6%
34
Sepharose Fast Flow
Agarose 6%
90
Sepharose 4 Fast Flow
Agarose 4%
90
Sepharose XL
Agarose 6%, dextran chains

coupled to agarose
90
Sepharose Big Beads
Agarose 6%
200
Capto ImpRes
High-flow agarose
40
Capto ImpAct
High-flow agarose
50
Capto
High-flow agarose
90
MiniBeads is a matrix made from polystyrene, with divinyl benzene as cross-linker, to produce
highly spherical (monodispersed), very small (3 m), nonporous particles that facilitate
micropreparative or analytical separations when extremely high resolution is more important
than high binding capacity or high flow rates.
MonoBeads and SOURCE are matrices made from polystyrene with divinyl benzene to produce
highly spherical (monodispersed), small (10, 15, or 30 m), porous particles (Fig 1.13) that
facilitate high resolution separations at high flow rates.
11000421 AC 21
Fig 1.13. Electron micrograph of MonoBeads showing spherical, monodispersed particles.
Sepharose media are based on chains of agarose, arranged in bundles and with different
degrees of cross-linking (Fig 1.14), to give a range of rigid, macroporous matrices with good
capacity and low nonspecific adsorption. The most suitable matrix can be selected according to
the degree of resolution, binding capacity, and flow rates desired for the separation. For example,
gradient elution on Sepharose High Performance (34 m) will give a high-resolution separation
whereas the larger particles of Sepharose Fast Flow (90 m) or Sepharose Big Beads (200 m)
would be most suited to high-capacity step elution at high flow rate.
Fig 1.14. Structure of cross-linked agarose media (Sepharose).
Capto media are based on a chemically modified, high-flow agarose matrix. This matrix provides
particle rigidity without compromising pore size, outstanding pressure/flow properties, and
high chemical stability to support CIP procedures. Capto media are suitable for scaling up and
for use in large-scale bioprocess purifications. The basic characteristics of Capto (90 m), Capto
ImpAct (50 m), and Capto ImpRes (40 m) IEX media are summarized in Chapter 3.
22 11000421 AC
Functional groups
The functional groups substituted onto a chromatographic matrix (Table 1.2) determine the
charge of an IEX medium, that is, a positively charged anion exchanger or a negatively charged
cation exchanger.
Table 1.2. Functional groups used on ion exchangers
Anion exchangers
Functional group
Quaternary ammonium (Q)
strong
-CH2-N+-(CH3)3
Diethylaminoethyl (DEAE)*
weak
-CH2-CH2-N+-(CH2-CH3)2
Diethylaminopropyl (ANX)*
weak
-CH2-CHOH-CH2-N+-(CH2-CH3)2
Cation exchangers
Functional group
Sulfopropyl (SP)
strong
-CH2-CH2-CH2-SO3-
Methyl sulfonate (S)
strong
-CH2-SO3-
Carboxymethyl (CM)
weak
-CH2-COO -
* The active end of the charged group is the same for DEAE and ANX. The difference between them is in the length of the
carbon chain of the charged group. DEAE has a diethylaminoethyl group bound to the agarose. ANX has a diethylaminopropyl
group attached which prevents the formation of quaternary groups, giving a different selectivity compared to DEAE.
The terms strong and weak refer to the extent that the ionization state of the functional
groups varies with pH. The terms strong and weak do not refer to the strength with
which the functional groups bind to proteins. Strong ion exchangers show no variation
in ion exchange capacity with change in pH (Fig 1.15). These exchangers do not take
up or lose protons with changing pH and so have no buffering capacity, remaining
fully charged over a broad pH range. Strong ion exchangers include Q (anionic), S, and
SP (cationic).
12
12
10
pH
pH
10
SP Sepharose Fast Flow
2
1
4
5
3
100 mM NaOH (ml)
4
5
3
100 mM NaOH (ml)
Fig 1.15. Titration curves show the ion exchange capacity of strong ion exchangers Q and SP.
Approximately 5 ml of Q or SP Sepharose Fast Flow were equilibrated in 1 M KCl and titrated with 100 mM NaOH.
There are several advantages to working with strong ion exchangers:

Development and optimization of separations is fast and easy since the charge
characteristics of the medium do not change with pH.
The mechanism of interaction is simple since there are no intermediate forms of
charge interaction.
Sample loading (binding) capacity is maintained at high or low pH since there is no
loss of charge from the ion exchanger.
11000421 AC 23
The majority of proteins have pI within the range 5.5 to 7.5 and can be separated on either
strong or weak ion exchangers. An advantage of a weak ion exchanger, such as DEAE (anionic),
ANX (anionic), and CM (cationic) is that they can offer a different selectivity compared to strong
ion exchangers. A disadvantage is that because weak ion exchangers can take up or lose
protons with changing pH, their ion exchange capacity varies with pH (Fig 1.16).
DEAE Sepharose Fast Flow
CM Sepharose Fast Flow
12
10
10
pH
pH
12
2
400
200
600
800
1000
200
400
600
800
1000
100 mM NaOH (ml)
100 mM NaOH (ml)
ANX Sepharose 4 Fast Flow (high sub)
12
10
pH
8
6
4
2
0
4 5 6 7 8
100 mM NaOH (ml)
10 11 1 2
Fig 1.16. Titration curves show how the ion exchange capacity of weak ion exchangers varies with pH.
Try a weak ion exchanger such as DEAE, CM, or ANX Sepharose Fast Flow, if a strong ion
exchanger (substituted with Q, S, or SP) does not give the required selectivity.
Binding capacity and recovery

The capacity of an IEX medium is a quantitative measure of its ability to take up counterions
(proteins or other charged molecules). The total ionic capacity is the number of charged
functional groups/ml medium, a fixed parameter of each medium. Of more practical relevance
is the actual amount of protein that can bind to an IEX medium, under defined experimental
conditions. The capacity of a chromatography medium can be measured in two ways: static
binding capacity (SBC) and dynamic binding capacity (DBC). SBC is the maximum amount of
protein that can bind at given conditions. SBC is often obtained during excess load of sample.
DBC is measured during given conditions, including flow rate, and is the amount of protein
that binds before a significant breakthrough of the target protein appears. Figures for binding
capacity in this handbook refer to the dynamic binding capacity.
The static and dynamic binding capacities depend upon the properties of the protein, the IEX
medium, and the experimental conditions. The capacity of an IEX medium will vary according
to the molecular size of the specific protein (which affects its ability to enter all the pores of
the matrix) and its charge/pH relationship (the protein must carry the correct net charge at
a sufficient surface density at the chosen pH). With earlier IEX media, larger biomolecules
had limited access to the functional groups, significantly reducing the binding capacity.
24 11000421 AC
Nowadays, ion exchange matrices such as MonoBeads, Capto, SOURCE, and Sepharose media
all have exclusion limits for globular proteins in excess of 1 106 and are therefore suitable
for the majority of biomolecule separations. Binding capacities will still vary according to the
molecular size of the biomolecules. For example, a matrix with a high degree of small pores
will exhibit a higher binding capacity for smaller molecules. Experimental conditions such
as pH, ionic strength, counterion, flow rate, and temperature should all be considered when
comparing binding capacities of different IEX media.
Modern IEX media show very low levels of nonspecific adsorption so that sample recovery
under suitable separation conditions is very high, typically between 90% and 100%.
Chromatofocusing
Chromatofocusing (CF) is a purification method separating proteins on the basis of differences
in their isoelectric points (pI). The matrix is usually a weak anion exchanger in which the
functional groups are amines. The eluent is a buffer containing a large number of buffering
substances which together give a uniform buffering capacity over a broad pH range. A pH
gradient is generated on the column as buffer and medium interacts. Proteins with different
pI values migrate at different rates as the pH gradient develops, continually binding and
dissociating while being focused into narrow bands and finally eluted.
CF is a powerful method and can resolve very small differences in pI (down to 0.02 pH units)
and thus separates very similar proteins. However, the capacity of the method is low and
should preferably only be used for partially pure samples. CF can be considered if IEX or other
methods do not give satisfactory purification.
11000421 AC 25
26 11000421 AC
Chapter 2
Ion exchange in practice
Introduction
This chapter includes practical advice on how to control experimental conditions to achieve a
successful separation and guidelines for selection of the most appropriate medium or prepacked
column for each application. The final resolution of an ion exchange (IEX) separation is
determined by selectivity and column efficiency. These parameters are influenced in turn by factors
such as particle size, porosity and column packing. The separation is influenced by a number
of factors, for example, the way in which the net surface charge of each protein in the sample
varies with pH, the pH and ionic strength of buffers, and the elution conditions. Understanding
the role and importance of each parameter ensures that every separation can be performed
with the required resolution, throughput and speed. Additional application examples and
product-related information are found in Chapter 3.
Selecting chromatography media

The origin and differences between modern IEX matrices are explained in Chapter 1. Choice of
a suitable matrix depends on factors such as the scale of the final purification, the purpose of
the separation (for example to concentrate sample in a capture step or to achieve high resolution
in a final polishing step) and the throughput required. Refer to Chapter 4 for more details on the
use of capture, intermediate purification, and polishing steps in a purification strategy.
Capture
When IEX is used as a capture step, the objective is to quickly absorb the protein(s) of interest
from the crude sample and isolate them from critical contaminants such as proteases. The
target protein(s) are concentrated and transferred to an environment that will conserve
potency/activity. Removal of other critical contaminants can also be achieved by careful
optimization of pH and elution conditions.
The focus is on capacity and speed in a capture step. It is advisable to compromise on the
potential resolution that can be achieved by an IEX separation to maximize the capacity and/or
speed of the separation in this first step (Fig 2.1).
Intermediate purification
When IEX is used for intermediate purification, the objective is to remove most of the significant
impurities such as proteins, nucleic acids, endotoxins, and viruses. In a typical intermediate
purification step, speed is less critical since sample volume has been reduced and damaging
contaminants have been removed during capture. Focus is on capacity and resolution in order
to maintain productivity and to achieve as high selectivity (purity) as possible (Fig 2.1).
Polishing
When IEX is used for polishing, most impurities have been removed except for trace amounts
or closely related substances such as structural variants of the target protein, nucleic acids,
viruses, or endotoxins. The purpose of the separation is to reduce these variants and trace
contaminants to acceptable levels for the application. In contrast to capture steps where fast,
high capacity, step elution is most commonly used, a polishing step will therefore focus on
achieving the highest possible resolution (Fig 2.1).
11000421 AC 27
Polishing
Remove trace impurities or

closely-related substances
Sample condition:
almost pure
Highest resolution g/run
MiniBeads (Q or S)
Highest resolution mg/run
MonoBeads (Q or S)
SOURCE 15 (Q or S)
High resolution and throughput
Wider pH stability window
SOURCE 30 (Q or S)
Intermediate
purification
Remove bulk impurities

Sample condition:
partially purified
High resolution
Easy scale-up
Sepharose High Performance (Q or SP)
High resolution and throughput

Flexibility of process design
Capto ImpRes (Q or SP)

Capto S ImpAct
Easy scale-up, Broad choice of

selectivity, including alternatives
to Q or S IEX media
Sepharose Fast Flow

(Q, SP, DEAE, CM, ANX)
High volume throughput and

high capacity, Easy scale-up
Capto (Q, S, DEAE, adhere, MMC)
High binding capacity for

selected proteins, Easy scale-up
Sepharose XL (Q or SP)
Large scale, viscous samples
Sepharose Big Beads (Q or SP)
Capture
Isolate, concentrate, and

stabilize target protein(s)
Sample conditions:
clarified or nonclarified
Fig 2.1. A typical purification strategy has three phases: Capture, Intermediate Purification, and Polishing (CIPP).
Each phase has a specific objective, dependent largely on the properties of the starting material. The
appropriate IEX medium is selected according to the objective of the purification step and the condition of
the starting material.
28 11000421 AC
A 280
5.0
Use for intermediate

purification if column
capacity is sufficient and
no scale-up is required.
Can be used for capture
steps if sample is free from
particulate matter.
Sample:
Pancreatin
Gradient elution
Mini Q (column 4.6 50 mm)
10.0
15.0
ml
A 280
Sample:
Pancreatin
Gradient elution
Mono Q (column 5 50 mm)
10
20
30
min
A 280
Sample:
Pancreatin
Gradient elution
RESOURCE Q, 1 ml
Use SOURCE 15 when

resolution is top priority.
0
10
20
30
min
A 280
Use HiTrap columns

prepacked with
Sepharose High
Performance, Sepharose
XL and Sepharose Fast
Flow for media selection
and pH scouting.
Sample:
Pancreatin
Gradient elution
SOURCE 30Q (HR 16 50 mm)
Use SOURCE 30 when

speed is top priority.
0
10
20
30
min
A 280
Sample:
Pancreatin
Gradient elution

(HR 16 50 mm)
10
20
30
Resolution
Use for intermediate

purification if column
capacity is sufficient
and no scale-up is required.
min
Use Capto ImpRes and

Capto S ImpAct for
increased productivity in
large-scale production
Try weak ion exchangers
such as DEAE, CM, or
ANX if the selectivity of
Q or S is unsatisfactory.
A 280
Sample:
Pancreatin
Gradient elution

(HR 16 50 mm)
10
20
30
min
Use high bed heights for

increased productivity.
Use Capto MMC for high
salt feed.
A 280
Use for capture with high

binding capacity/rapid
separation of proteins from
clarified samples
Q Sepharose XL
5.0
10.0
15.0
20.0
Volume (l)
Sample:
Recombinant a-amylase
Pilot scale:
Gradient elution begins
after 20 l
Use with step elution.
11000421 AC 29
Fast IEX media selection and method development
Fig 2.2. HiTrap IEX Selection Kit contains seven HiTrap columns prepacked with different Sepharose
Fast Flow media. The kit is an excellent choice for screening of the most appropriate media and conditions
to use in application and development work.
Time and sample can be saved in the early stages of development by using small, prepacked
columns such as those in the HiTrap IEX Selection Kit (Fig 2.2). The kit allows quick and efficient
screening for the most suitable charge group and enables development of the basic separation
method (see Appendix 11, Media selection). This approach is particularly helpful if the properties of
the target protein(s) are unknown.
HiTrap columns can be run with a syringe, a peristaltic pump, or any KTA chromatography
system. HiTrap columns can be used for small-scale purification as well as fast method
development and are supplied with detailed protocols for use.
The HiScreen column format has been specially designed for screening and optimizing before
scaling up the purification. The higher bed height of HiScreen (10 cm), in comparison with
HiTrap (2.5 cm), is suitable for scaling up while keeping the bed height constant.
Practical considerations for IEX separation

This section covers detailed aspects of each step in an IEX separation, together with practical hints
and tips to improve resolution and overall performance.
Buffer pH and ionic strength

Buffer pH and ionic strength must be compatible with protein stability and activity. The most
suitable pH should allow the proteins of interest to bind, but should be as close to the point of
release (elution) as possible. If the pH is too low or too high, elution becomes more difficult and
high salt concentrations might be needed. This should be avoided since some proteins begin
to precipitate at high ionic strength and high salt concentrations can interfere with assays or
subsequent chromatographic steps.
Avoid extreme changes in pH or other conditions that can cause inactivation or even
precipitation.
The pH and ionic strength of the sample are extremely important in order to achieve the
most effective high resolution or group separations and to make the most of the high loading
capacity. Samples should preferably be buffered in the start buffer (see Appendix 1, Sample
preparation for details). When working with small volumes during screening and scouting, it
might be sufficient to dilute the sample in start buffer in order to lower the ionic strength and
adjust the pH to a value similar to that of the start buffer.
30 11000421 AC
Proteins often begin to dissociate from IEX media about 0.5 pH units from their pI at an ionic
strength around 100 mM. The pH of the start buffer should be at least 0.5 to 1.0 pH unit above
the pI of the target substance when using an anion exchanger (Q, DEAE, or ANX) or 0.5 to 1.0 pH
unit below the pI of the target substance when using a cation exchanger (SP or CM).
For samples with unknown charge properties, try the following strong ion exchangers first:
anion exchange (Q)
start buffer: pH 8.0
elution buffer: start buffer including 1 M NaCl, pH 8.0
cation exchange (S, SP)
start buffer: pH 6.0
See Appendix 2 for recommendations on volatile and nonvolatile buffer systems for anion and
cation exchangers.
Whenever possible, check for stability at the pH and ionic strength values selected,
especially if recovery of biological activity is a priority.
Anion or cation exchanger

For molecules such as nucleic acids, which carry only negatively charged groups, an anion
exchanger is the obvious choice. However, since the net charge of molecules such as proteins
(carrying positively and negatively charged groups) depends on pH, the choice is based on
which type of exchanger and pH give the desired resolution within the constraints of sample
stability. For example, Figure 2.3 shows a theoretical protein which has a net positive charge
below its pI, and can bind to a cation exchanger. Above its pI, the protein has a net negative
charge and can bind to an anion exchanger. However, the protein is only stable in the pH range
between 5.0 and 8.0 and so an anion exchanger has to be used.
+
pI
Net charge of protei n
Range of
stability
Attached 4
to cation
exchangers
Attached to
anion exchangers
6
10
pH
Fig 2.3. Considerations when selecting a suitable IEX medium.
If sample components are most stable below their pI, use a cation exchanger.
If sample components are most stable above their pI, use an anion exchanger.
If stability is high over a wide pH range on both sides of the pI, use either type of
ion exchanger.
11000421 AC 31
Strong or weak ion exchangers

Table 2.1 shows the functional groups used on IEX media. The terms strong and weak refer to
the extent that the ionization state of the functional groups varies with pH. The terms strong and
weak do not refer to the strength with which the functional groups bind to proteins.
Table 2.1. Functional groups used on ion exchangers
Anion exchangers
Functional group
Quaternary ammonium (Q)
strong
-CH2-N+-(CH3)3
Diethylaminoethyl (DEAE)
weak
-CH2-CH2-N-(CH2-CH3)2
Diethylaminopropyl (ANX)
weak
-CH2-CHOH-CH2-N-(CH2-CH3)2
Cation exchangers
Functional group
Sulfopropyl (SP)
strong
-CH2-CH2-CH2-SO3-
Methyl sulfonate (S)
strong
-CH2-SO3-
Carboxymethyl (CM)
weak
-CH2-COO -
The active end of the charged group is the same for DEAE and ANX. The difference between them is in the length
of the carbon chain of the charged group. DEAE has a diethylaminopropyl group bound to the agarose. ANX has a
diethylaminopropyl group attached, which prevents the formation of quaternary groups giving a different selectivity
compared to DEAE.
Begin with a strong ion exchanger to enable development work to be performed over
a broad pH range. Use a strong anion exchanger (Q) to bind the protein(s) of interest if
their pI is below pH 7.0 or unknown.
Use a strong ion exchanger in cases where maximum resolution occurs at an extreme
pH and the proteins of interest are stable at that pH.
Consider using a weak exchanger if the selectivity of the strong ion exchanger is
unsatisfactory, but remember that the ion exchange capacity of a weak ion exchanger varies
with pH. As a result:
Sample loading (binding) capacity can vary with increasing pH due to loss of charge from
the exchanger.
Resolution is more readily affected by changes in flow rate or sample load due to the
intermediate forms of charge interaction that can occur.
Predicted results (based on known information about the sample components such as their
pI and how their net surface charge changes with pH) might not correlate with actual results
since the number of charged groups on weak ion exchangers can vary with pH.
Longer equilibration times might be required in order to titrate the weak ion exchange
functional groups.
When using a weak exchanger, work within the pH values given below to minimize
variations in performance:
DEAE:
ANX:
CM:
32 11000421 AC
pH 2.0 to 9.0
pH 2.0 to 9.0
pH 6.0 to 10.0
Buffer selection and preparation

Buffer ions
Buffering ions should have the same charge as the functional groups on the IEX medium
(buffering ions that carry a charge opposite to that of the functional groups will take part
in the ion exchange process and can cause significant pH fluctuations during elution) and,
preferably, a pKa value within 0.6 pH units of the working pH. An exception to this rule is
seen in the frequent use of phosphate buffers with anion exchange separations. However,
phosphate buffers must be very carefully prepared to ensure reproducibility between batches.
Use a buffer concentration that is sufficient to maintain buffering capacity and constant
pH, typically 20 to 50 mM.
Use volatile buffers if the purified product is to be lyophilized.
See Appendix 2 for recommendations on volatile and nonvolatile buffer systems for anion and
cation exchangers.
Filter buffers after all salts and additives have been included. Use high quality water
and chemicals. Filter solutions through 1 m filters for particle sizes above 90 m,
0.45 m filters for 34 m particles, or 0.22 m filters for particles sizes below 15 m or
when sterile or extra clean samples are required. To avoid formation of air bubbles in
a packed column, ensure that column and buffers are at the same temperature when
preparing for a run.
Effect of temperature on buffer pH

Select buffers that have appropriate pKa values for the working temperature. The pKa of
a buffering substance varies with temperature. For example, Tris has a pKa of 8.85 at 0C, 8.06 at
25C and 7.72 at 27C. Using Tris at 4C at a pH 7.9 would give a very low buffering capacity and
the working pH would be outside the useful pH range (pKa + 0.5) of the buffer.
Prepare buffers at the same temperature at which they will be used.
Temperatures < 10C can minimize aggregation caused by hydrophobic interactions
between sample components. Working at these lower temperatures can be an
alternative solution to using a detergent to improve solubility.
Counterions
Counterions (salt ions) used in IEX are almost always Na+ for cation exchange and
Cl for anion exchange.
Salts such as NaCl have a chaotropic character (i.e., an ability to make water less polar) and
therefore a lower salting-out effect on hydrophobic molecules. This ensures maximum
solubility during elution and improves recovery. Chaotropic salts can also be used in the
presence of organic solvents if required. Salts such as (NH4)2SO4 or K3PO4 should be avoided as
they are most likely to cause precipitation at high concentrations.
In certain applications alternative counterions such as Li+, Br, I, SO42, CH3COO, or HCOO can
improve and even alter, selectivity since they exhibit different elution strengths, but it should be
noted that using these ions might affect the binding capacity of the medium. Figure 2.4 shows
how selectivity and resolution can vary when using different counterions.
11000421 AC 33
Column:
Sample:
Mono Q HR 5/5
carbonic anhydrase, transferrin, ovalbumin, a-lactalbumin, b-lactoglobulin A and B
(A)
(B)
1
2
A 280 nm
6
5
14.8 ml
0.28 M NaBr
6
5
Volume (ml)
Volume (ml)
(C)
(D)
1
3
4
0.7 M NaOAc
Volume (ml)
6
15.0 ml
Elution buffer concentration
34
0.25 M Nal
6
14.6 ml
A 280 nm
A 280 nm
14.6 ml
0.35 M NaCl
A 280 nm
Volume (ml)
Fig 2.4. Effect of salt ions (counterions) (A) sodium chloride, (B) sodium bromide, (C) sodium iodide, and (D)
sodium acetate on selectivity and resolution (Mono Q HR 5/5 now available as Mono Q 5/50 GL). Note the
variation in elution order of peaks 3 and 4.
Use the following procedure if the medium is to be used with counterions other than
Na+ or Cl-:
1. Wash the packed column with 10 CV of 0.5 to 1.0 M salt solution containing the new
counterion. Flow rate: see relevant IEX media section in Chapter 3.
2. Wash with 10 CV of start buffer at the same flow rate as in step 1.
3. Repeat steps 1 and 2 several times.
Perform a blank run to check conductivity and pH.
Flow rates
The maximum flow rate applied during a separation can vary according to the stage of the
separation. For example, during sample application and elution, lower flow rates allow time
for sample components to diffuse in and out of the pores as they to bind to or dissociate from
the functional groups. Figure 2.5 shows an example of the influence of flow rate on resolution.
Higher flow rates can be used for equilibration, washing and re-equilibration, limited primarily
by the rigidity of the media and by pressure specifications of the equipment.
Recommended flow rates for each chromatography medium are given in Chapter 3. Working
from these recommendations, select the highest flow rate that maintains resolution and
minimizes separation time. For example, if peaks are well separated at a low flow rate, increase
the flow rate or alternatively, increase the sample volume to benefit from a higher capacity
without significant loss of resolution.
34 11000421 AC
Flow rate can be measured as volumetric flow rate, that is, volume per unit time (ml/min). When
when comparing results between columns of different sizes or when scaling-up, it is useful to
use flow velocity, which measures the flow rate (ml/min) divided by the cross-sectional area of
the column and is expressed as flow velocity time (for example, cm/h, see Appendix 5). Results
obtained at the same flow velocity on different size columns will be comparable.
Save time by using higher flow rates during the high salt wash and re-equilibration
steps. Do not exceed the maximum recommended flow for the medium.
Higher flow rates and viscous buffers increase operating pressures (remember that
buffer viscosity increases when running at 4C). Check the maximum operating
pressure of the packed column and set the upper pressure limit on the chromatography
system accordingly.
Column:
Sample:
Sample load:
Start buffer:
Elution buffer:
Flow rates (flow velocities):
Gradient:
SOURCE 30Q, 10 mm i.d. 50 mm (4 ml)

Mixture of lactoglobulin B and amyloglucosidase
1 mg/ml of bed volume
20 mM BIS-Tris PROPANE, pH 7.0
500 mM sodium chloride, 20 mM BIS-TRIS PROPANE, pH 7.0
(A) 4 ml/min (300 cm/h)
(B) 13 ml/min (1000 cm/h)
0% to 100% elution buffer, 20 CV
A 280 nm
(B)
A 280 nm
(A)
10
20
Time (min)
4
Time (min)
Fig 2.5. Influence of increasing flow rate on resolution.
Flow control
Accurate, reproducible flow control is essential for good resolution and reproducibility.
Use a pump within a chromatography system (rather than a peristaltic pump) to fully utilize
the high rigidity and excellent flow properties of the medium.
If you have packed the column yourself, always use a flow rate for separation that
is less than the flow rate used for column packing in order to avoid shrinking of the
column bed by pressure increases that can occur when running a sample.
11000421 AC 35
Steps in an IEX separation

The six steps listed are described in more detail throughout this section.
1. Equilibrate column with 5 to 10 CV of start buffer or until the baseline, eluent pH, and
conductivity are stable.
2. Adjust the sample to the chosen starting pH and ionic strength and apply to the column.
3. Wash with 5 to 10 CV of start buffer or until the baseline, eluent pH, and conductivity are
stable, that is, when all unbound material has washed through the column.
4. Begin elution using a gradient volume of 10 to 20 CV with an increasing ionic strength
up to 500 mM NaCl (50%B). Alternatively, elute bound proteins with 5 CV of start buffer +
NaCl at chosen ionic strength. Repeat at higher ionic strengths until the target protein(s)
has been eluted.
5. Regeneration: Wash with 5 CV of 1 M NaCl (100%B) to elute any remaining ionically bound
material.
6. Re-equilibrate with 5 to 10 CV of start buffer or until eluent pH and conductivity reach the
required values.
Buffer volumes referred to are expressed in column volumes, for example 3 CV = 3 ml for
a column with a 1 ml bed volume. Using CV to describe a separation profile facilitates
method development and transfer of methods to columns of different dimensions.
The number of CV used at each stage of the separation can often be reduced by
optimization. For example, less buffer is required to equilibrate a strong ion exchanger,
the gradient volume can be reduced if resolution can be maintained and less buffer might
be required for washing when separating less complex and reasonably clean samples.
Column and media preparation

Using prepacked columns is highly recommended to ensure the desired high performance
and reproducible results. An evenly packed column ensures that component peaks are not
unnecessarily broadened as sample passes down the column so that optimal resolution can
be achieved.
Allow buffers, media or prepacked columns to reach the same temperature before
use. Rapid changes in temperature, for example removing packed columns from a
cold room and then applying buffer at room temperature, can cause air bubbles in the
packing and affect the separation.
Wash away storage solutions and preservatives before using any IEX medium.
Increase the volumes used for column equilibration before the first run if using buffers
containing detergents or a different counterion to the one in which the medium has
been stored.
Appendix 3 gives details on column packing. The volume required for the packed bed is determined
by the amount of sample to be purified and the binding capacity of the medium. Pack a column that
will have approximately five-fold excess of the binding capacity required with a bed height up
to 20 cm.
Check column performance regularly by determining column efficiency and peak
symmetry. See Appendix 3. Note that this does not apply to HiTrap or HiPrep columns.
36 11000421 AC
Sample preparation
Correct sample and buffer preparation is essential in order to achieve optimal separation
and avoid any deterioration in column performance. Simple steps to clarify a sample before
application to a column will avoid the risk of blockage and reduce the need for stringent
washing procedures. Appendix 1 contains a detailed overview of sample preparation techniques.
Desalt samples and transfer into the chosen start buffer (see Buffer exchange and
desalting in Appendix 1). The pH and ionic strength of the sample are extremely
important in order to achieve the most effective high resolution or group separations
and to make the most of the high loading capacity.
For small sample volumes in a high salt concentration and with no major contaminants
such as lipids or ionic detergents, it might be sufficient to dilute the sample with start
buffer in order to lower the salt concentration to a level that does not interfere with
binding to the medium. However, buffer exchange and desalting is the only way to
guarantee the correct pH and ionic strength conditions of a sample.
Samples must be clear and free from particulate matter, particularly when working with
particle sizes of 34 m or less. For small sample volumes, a syringe-tip filter of cellulose
acetate or PVDF can be sufficient for sample filtration.
Sample concentration and viscosity

The solubility or viscosity of the sample can limit the quantity that can be applied to a column.
High sample viscosity can cause instability of the separation and an irregular flow pattern
resulting in broad, distorted peaks, and problems with back pressure. The critical parameter is
the viscosity of the sample relative to the viscosity of the eluent.
Dilute viscous samples with start buffer. If high viscosity is caused by the presence of
nucleic acid contaminants, see Appendix 1 for advice on their removal. Remember that
viscosity varies with temperature. If dilution is not an option, using a medium with a
larger particle size can help to overcome viscosity problems.
Samples should generally not exceed 50 to 70 mg/ml protein, but can vary according to
the type of sample and the type of chromatographic medium.

Starting conditions should maximize binding of the target proteins near the top of the column
and, when possible, minimize binding of contaminants so that they pass through the column.
For efficient binding the sample should be at the same pH and ionic strength as the
start buffer. The sample volume can be relatively large without affecting the separation
since the sample will bind at the top of the column as long as equilibration and sample
conditions are correct.
Apply samples directly to the column via a chromatography system, a peristaltic pump,
or a syringe. The choice of equipment depends largely on the sample volume, the size of
column, the type of IEX medium, and the requirements for accuracy in gradient elution.
Ensure that the top of the column bed is not disturbed during sample application.
Do not change buffer conditions until all unbound material has been washed through
the column (monitored by UV absorbance) and until UV and conductivity values have
returned to starting conditions.
11000421 AC 37
Sample load
Sample load (mass) is of greater importance than sample volume. The amount of sample which
can be applied to a column depends on the dynamic binding capacity of the IEX medium and the
degree of resolution required. Sample load has a major influence on resolution since the width
of the peaks is directly related to the amount of substance present, as shown in Figure 2.6.
Consequently, in order to achieve satisfactory resolution, the total amount of protein applied
and bound to the medium should not exceed the total binding capacity of the packed column.
Column:
Sample:
Sample load:
Start buffer:
Elution buffer:
Flow rate (flow velocity):
Gradient:
SOURCE 30S, 5 mm i.d. 50 mm (1 ml)

Mixture of chymotypsinogen, cytochrome C, and lysozyme
(A) 1 mg
(B) 10 mg
20 mM sodium phosphate, pH 6.8
500 mM sodium chloride, 20 mM sodium phosphate, pH 6.8
1 ml/min (300 cm/h)
A 280 nm
(B)
A 280 nm
(A)
10
Time (min)
20
10
Time (min)
20
Fig 2.6. The influence of increasing sample load on resolution.
Apply up to 30% of the total binding capacity of the column for optimal resolution with
gradient elution. Sample loads can be increased if resolution is satisfactory or when
using a step elution.
If sample volumes are large compared to the total CV, the sample buffer composition,
in particular the ionic strength, should be the same as that of the start buffer to ensure
adequate binding conditions.
Chapter 3 gives typical binding capacities for each medium as a guideline for total binding capacity.
The actual (dynamic) binding capacity is also affected by factors such as size and shape of the
molecules, the pore size of the matrix, flow rate, sample concentration, pH/protein charge, and
ionic strength. Capacity will decrease for molecules of very large diameter or length such as
protein complexes > Mr 400 000 asymmetric proteins, and DNA. These molecules are unable
to penetrate the matrix pores, limiting their binding primarily to the charged groups on the
surface of the matrix. Since the exact distribution of pore sizes in some matrices can vary and
the apparent size of a molecule can vary according to the buffer conditions, there is no distinct
molecular weight cut-off point when molecules can or cannot penetrate the matrix pores.
The binding step and the dynamic binding capacity can be increased by applying
sample at a pH where the target protein has a higher charge than if the optimal pH for
separation was used.
38 11000421 AC
Sample volume
As a binding technique, IEX is independent of sample volume as long as the ionic strength
of the sample is the same or as low as the start buffer and the target proteins are sufficiently
charged at the selected pH. Large volumes of dilute solutions such as fractions from a
desalting step or a cell culture supernatant can be applied directly to an IEX medium without
prior concentration.
Elution of target protein

Bound proteins are eluted by controlled changes in ionic strength or pH. The way in which
these changes take place, by using a linear or step elution, is selected according to the aim of
the separation.
Linear gradient elution allows high-resolution separation/analysis. Step elution ensures faster
separation time with reduced buffer consumption as well as group separation.
Linear gradient elution

For high-resolution separation/analysis, elution is performed using a linear gradient volume of
10 to 20 CV with an increasing ionic strength up to 500 mM NaCl (50%B).
equilibration
sample
injection
volume
gradient
elution
regeneration
NaCl concentration
1M
5 CV
tightly bound
molecules
elute in high
salt wash
10 to 20 CV
5 to 10 CV
re-equilibration
high salt wash
5 to 10 CV
Column volumes (CV)
Fig 2.7. Typical IEX separation using linear gradient elution. The UV (protein) and conductivity (salt) traces
show the elution of protein peaks and the changes in salt concentration during elution.
Linear ionic strength gradients, as shown in Figure 2.7, are the most frequently used type
of elution and should always be used when starting with an unknown sample (when as many
components as possible are bound to the column and eluted differentially to see a total
protein profile). At low ionic strengths, competition for charged groups on the IEX medium is at
a minimum. Increasing the ionic strength increases competition and reduces the interaction
between the medium and the bound substances, which begin to elute. The elution buffer is
usually the same buffer salt and pH as the start buffer, but contains additional salt, most often
sodium chloride.
Use of linear gradient elution during method development is strongly recommended.
Linear ionic strength gradients are easy to prepare and very reproducible when
generated by a suitable chromatography system. The results obtained can then serve
as a base from which to optimize the separation.
The retention of charged proteins on the IEX medium is related to the volume of the column
and the concentration difference across it:
Long, shallow gradients give maximum separation between peaks, but separation times will
be longer and there will be greater peak broadening.
11000421 AC 39
Short, steep gradients give faster separations and sharper peaks, but peaks will be eluted
closer together.
Peaks eluted later in the gradient tend to be slightly broader than those eluted early on.
Select the steepest gradient to give acceptable resolution at the selected pH.
The effects of gradient slope are shown in Figure 2.8.
Column:
Sample:
Start buffer:
Elution buffer:
Flow rate:
Mono Q HR 5/5
Partially purified dynorphin-converting enzyme
20 mM Tris, pH 7.0
20 mM Tris, 1 M NaCl, pH 7.0
1 ml/min
(A)
(B)
Gradient 0% to 100% elution buffer in 20 CV
Gradient 0% to 40% elution buffer in 20 CV

0.10
A 280 nm
A 280 nm
0.15
0.10
0.05
0.05
0.00
0.00
0.0
10.0
20.0
30.0
0.0
10.0
20.0
30.0
Ionic strength
Time (min)
Ionic strength
Time (min)
Elution volume
Elution volume
Fig 2.8. Effect of gradient slope on resolution, in theory and in practice.
If gradient elution volumes are decreased, it might be necessary to decrease the

sample load proportionally in order to maintain the same resolution. Similarly, if sample
load is increased (within the total capacity of the column), gradient volumes might need
increasing to maintain resolution.
Gradients are most efficiently formed using KTA chromatography systems with
preprogrammed method templates, which automatically control the mixing of solutions
being supplied to a column.
Accurate buffer preparation, efficient mixing, and the shortest possible flow path
between a mixer and the top of a column will help to ensure accurate gradient formation.
For certain separations, when conditions for a high-resolution separation using a linear
gradient have been established, it might be possible to reduce the total separation time by
using a more complex elution profile while maintaining resolution (Fig 2.9). Shallow gradients
can be used where maximum resolution is required while steeper gradients can be used in
areas where resolution is satisfactory.
40 11000421 AC
high salt wash
1M
5 CV
NaCl concentration
shallow
gradient
step
gradient
sample
injection
volume
10 to 20 CV
re-equilibration
equilibration
0
5 to 10 CV
5 to 10 CV
Column volumes (CV)
Fig 2.9. Complex gradient profiles can reduce total separation time for certain separations.
Step elution
high salt wash
NaCl concentration
1M
sample
injection
volume
unbound
molecules
elute
elution of
unwanted
material
elution
of target
molecule
5 CV
tightly bound
molecules
elute
5 CV
equilibration
re-equilibration
5 to 10 CV
0
5 CV
5 to 10 CV
Column volumes (CV)
Fig 2.10. Typical IEX separation using step elution. The UV (protein) and conductivity (salt) traces show the
elution of protein peaks and the changes in salt concentration during elution.
As shown in Figure 2.10, step elutions are performed by sequential addition of the same buffer
at increasing ionic strengths. Step elution is technically simple, but care must be taken in the
design of the steps and the interpretation of results since substances eluted by a sharp change
in ionic strength elute close together, giving a false peak that can contain several components.
Peaks tend to have sharp fronts and pronounced tailing since they frequently contain more than
one component. Tailing can lead to the appearance of false peaks if a change in ionic strength is
introduced too early. For these reasons, use a linear ionic strength gradient when developing a
new method.
When an IEX separation has been optimized using gradient elution, changing to step elution
reduces the total number of CV used for a separation. This speeds up separation times and reduces
buffer consumption while retaining the required purity level. Step elutions of this type are often
used for routine, large-scale separation. An added advantage of a step elution when used at
larger scale is that it is often possible to apply a greater amount of sample, since the molecules
which would elute early in a gradient separation no longer take up binding capacity on the column.
In a group separation the molecules of interest are concentrated and rapidly removed from
unwanted substances. When binding and elution conditions for a target protein(s) and
contaminants have been determined, usually during preliminary gradient elution separations,
conditions are chosen to maximize binding of the target protein(s) and minimize binding of
contaminants during sample application. The target protein(s) is then eluted by a single buffer
change in an enriched, concentrated form. Figure 2.11 shows an example of such a separation
in which a HiTrap Q HP column is used to separate human serum proteins from the unwanted
IgG fraction, which passes directly through the column.
11000421 AC 41
Column:
Sample:
Sample volume:
Start buffer:
Elution buffer:
HiTrap Q, 1 ml
Human serum, filtered (0.45 m filter)
and buffer exchanged to start buffer
on a PD-10 column
1.0 ml
75 mM Tris-HCl, pH 8.0
75 mM Tris-HCl, 1.0 M NaCl, pH 8.0
0.5 ml/min, (75 cm/h)
100% Buffer B
1.0
0.8
pool 1
pool 2
A 280 nm
0.6
0.4
0.2
0
5
10
15
20
Volume (ml)
25
30
35
40
Fig 2.11. Group separation of serum proteins on HiTrap Q HP.
If starting conditions have been chosen to maximize the binding of contaminants, then
no change in elution conditions is required since the target protein(s) will pass through
the column. For many applications, it is preferable to discard the column rather than
spend time and effort removing unwanted bound substances.
pH elution
Since the net charge on a protein is pH-dependent, samples can also be eluted from an IEX
medium by altering the pH of the elution buffer. As there is no salt gradient, samples are simply
retained on the column at one pH and eluted by increasing or decreasing the pH. The various
charged groups in the sample or on the column are titrated until they are neutral or of opposite
charge to the medium and the sample elutes.
Proteins bound to an anion exchanger (Q, DEAE, ANX) will elute as pH is decreased.
Proteins bound to a cation exchanger (SP, S, CM) will elute as pH is increased.
Since pH elution will involve working at pH values close to the pl of a protein and since
many proteins show minimum solubility close to their pl, precautions must be taken to avoid
precipitation on the column (see Detergents, denaturing agents, and other additives later in this
chapter for information on the use of additives to avoid precipitation).
Always test in advance the solubility of sample components at the pH and salt
concentrations to be used during separation.
For any type of pH elution, care must be taken in the selection and mixing of buffer systems in
order to achieve reproducibility. Stepwise pH elution is easier to produce and more reproducible
than using a linear pH gradient. Note that for weak ion exchangers the buffer might have to
titrate the charged groups on the medium and there will be a short period of re-equilibration
before the new pH is reached.
42 11000421 AC
Linear pH gradients are very difficult to produce at constant ionic strength, since simultaneous
changes in ionic strength, although small, also occur. These gradients cannot be obtained
simply by mixing buffers of different pH in linear volume ratios since the buffering capacities of
the systems produced are pH-dependent. A relatively linear gradient can be produced over
a narrow pH interval (maximum 2.0 pH units) by mixing two solutions of the same buffer salt
adjusted to 1.0 pH unit above and 1.0 pH unit below the pKa for the buffer.
In general, separation of proteins according to their pI, using chromatofocusing, is likely
to provide a more reliable and higher resolution result than attempting to elute proteins
from an IEX column using a pH gradient.
Regeneration and re-equilibration

Include a wash step (regeneration) at the end of every run in order to remove any molecules
that are still bound to the medium. Monitor UV absorbance so that the wash step can be
shortened or prolonged, as necessary.
A re-equilibration step after washing returns the column to start conditions before applying
further samples. Whenever possible, monitor pH and conductivity to check when start conditions
have been reached. The re-equilibration step can then be shortened or prolonged as necessary.
Increase flow rates during wash and re-equilibration steps to save time between runs.
If ionic detergents have been used, wash the column with 5 CV of distilled water,
followed by 2 CV of 2 M NaCl. Re-equilibrate with at least 10 CV of start buffer until the
UV baseline, eluent pH, and/or conductivity are stable. Organic solvents such as ethanol
can be used to remove nonionic detergents. When selecting an organic solvent, check the
chemical stability of the medium to determine a suitable concentration.
Detergents, denaturing agents, and other additives

Any additives used for dissociation, solubilization, metal chelation, and enzyme
inhibition should always be checked for their charge characteristics at the working
pH. Run blank gradients with additives included in order to check their effect on the
chromatographic profile.
Additives used during sample preparation will be separated from the sample
components during IEX. If proteins are seen to precipitate, elute later than expected,
or are poorly resolved, add a suitable concentration of the additives used for initial
solubilization to the start and elution buffers.
Zwitterionic additives such as betaine can prevent precipitation and can be used at high
concentrations without interfering with the gradient elution.
Detergents are useful as solubilizing agents for proteins with low aqueous solubility such as
membrane components. Anionic, cationic, zwitterionic, and nonionic (neutral) detergents can
be used during IEX.
Denaturing agents such as guanidine hydrochloride or urea can be used for initial solubilization
of a sample and during separation. However, they should be avoided unless denaturation is a
requirement. Note that, at the pH values used for separation, guanidine is a charged molecule with
a counterion and will therefore participate in the ion exchange process in the same way as NaCl.
Examples of commonly used detergents and denaturing agents are given in Table 2.2.
11000421 AC 43
Table 2.2. Commonly used detergents and denaturing agents

Detergent
Urea
Type
Guanidine hydrochloride
Typical conditions
for use
Compatibility
2 to 8 M
anion or cation exchangers
3 to 6 M
Triton X-100
nonionic
2%
N-Octylglucoside
nonionic
2%
Sodium dodecyl sulfate
ionic
0.1% to 0.5%
exchange for nonionic detergent

during first chromatography step,
avoid anion exchangers
Sarcosyl1
anionic
1.5%
cation exchangers
Nonidet P40
nonionic
Polyoxyethylene ethers
(e.g., Brij 35)
nonionic
Polyoxyethylene sorbitans nonionic

(e.g., Tween 80)
CHAPS
zwitterionic, derivative
of cholic acid

(pH-dependent)
CHAPSO
zwitterionic, derivative
of cholic acid

(pH-dependent)
Deoxycholate
cation
anion exchangers
Sarcosyl is strongly protein-denaturing.
Temperatures < 10C can minimize aggregation caused by hydrophobic interactions

between sample components. Working at these lower temperatures is an alternative to
using a detergent to improve solubility.
Developing or optimizing a separation using buffers that contain detergents

1. Select detergents that are compatible with the sample. A detergent must be neutral,
zwitterionic, or have the same charge as the IEX medium. Detergents that bind to
the medium can be difficult to remove and can affect protein loading capacity, pH,
conductivity, and resolution.
2. Determine the minimum concentration that is likely to keep the sample in solution
during the separation. Note that different detergents will have different solubilization
properties resulting in different peak profiles.
3. Equilibrate the column thoroughly with the detergent solution, using a concentration
that is below the critical micelle concentration for the specific detergent.
4. Run blank salt gradients to determine the UV absorbance profile of the detergent and
to detect any effect pH. Micelle formation causes light scattering and the appearance
of a peak during UV monitoring. If micelle formation is a problem try the following:
- decrease detergent concentration as far as possible without impairing sample solubility
- increase detergent concentration to run the gradient above the critical micelle
concentration (this creates a gradual rather than abrupt UV increase)
- change the salt gradient so that the sudden change in UV absorption does not occur
during the run
- change to highly chaotropic salts such as lithium perchlorate or sodium trichloroacetate
that can be used at higher concentrations without causing micelle formation
5. Perform test runs with sample to find the detergent that gives optimal solubilization
and resolution.
44 11000421 AC
A single peak obtained from a detergent run often contains more than one
component and should be analyzed carefully. Selecting a different detergent might
improve the separation.
Detergent concentrations that are too high will increase buffer viscosity so that flow
rates must be reduced to avoid overpressure of the column. The concentration of
detergent required for solubilization can often be reduced during the separation.
Use detergents of the highest quality that are free from salts. Filter buffers that contain
detergents under weak suction and ultrasonication for degassing to avoid foaming.
Wash previously used columns thoroughly using recommended procedures before
working with buffers that contain detergents.
Reagents to reduce polarity

Monoethylene glycol, glycerol and similar mild reagents that reduce polarity can be included
in buffers. Avoid high concentrations (> 40% w/w) as buffer viscosity will increase and can
overpressure the column.
Metal chelators: EDTA, EGTA

EDTA (ethylenediaminetetracetic acid) and EGTA (ethylene glycol-bis-[2-aminoethyl]-N,N,N,Ntetraacetic acid) are often used in buffers as metal chelators and can be used with IEX. EDTA
and EGTA contain several carboxylic acid groups that interact with anion exchangers. During
anion exchange separations, EDTA and EGTA can concentrate as a band on the column
and elute during a salt gradient. Both molecules absorb UV and will appear as a peak or as
background noise in the chromatogram.
Analysis of results and further steps

The analysis of results from the first separation will indicate if conditions can be improved to
increase the yield, achieve higher purity, speed up the separation, or increase the amount of
sample that can be processed in a single run.
Samples eluted using a salt gradient will contain a range of salt concentrations. Dilute or desalt
fractions before analysis, if the assay is sensitive to changes in salt concentration.
Commonly used analytical assays are outlined in Appendix 8.
Scaling-up
For fast separations, it might be easier to repeat a separation several times on a small column
and pool the fractions of interest, rather than scale-up to a larger column. However, a larger
column can be preferred for routine processing of large sample volumes. General guidelines for
scaling-up are shown in Table 2.3.
Table 2.3. Guidelines for scaling-up
Maintain
Increase
Column bed height
Column volume, i.e., column diameter
Flow velocity (cm/h)
Flow rate (ml/min)
Sample concentration
Sample load
Gradient elution volume , i.e., number of

column volumes used for the gradient
11000421 AC 45
When scaling-up an IEX separation, follow the points below to ensure the same cycle time for
small scale and larger scale separations.
1. Optimize the separation at small scale.
2. Maintain bed height, sample concentration, and the ratio of sample volume:
volume of medium.
3. Increase the column volume by increasing the cross-sectional area (diameter) of the column.
4. Run the separation at the same flow velocity (see Appendix 5) as used on the smaller
column with the same ratio of gradient volume: column volume.
The HiScreen column format has been especially designed for screening and optimizing
before scaling up. The higher bed height of HiScreen (10 cm), in comparison with HiTrap
(2.5 cm), is suitable for scaling up while keeping the bed height constant.
During method development, a small particle size may be used to improve resolution.
However, smaller particles can also result in increased back pressure and this factor
can become restrictive when scaling-up. Consider using larger particles, preferably of
the same medium, to utilize lower back pressures and higher flow rates.
When scaling-up, the salt concentrations at which peaks elute can decrease with
increased sample loads. As sample is applied to the column, components with a low net
charge are displaced by components with a higher net charge. Molecules will elute in
the same order, but at a different point in the elution profile.
When method scouting, develop the method, whenever possible, on the medium that
will be used at the larger scale.
For production-scale separations which must satisfy throughput and cleaning-in-place
(CIP) requirements of the bioprocess industry, transfer an optimized method as early
as possible to a matrix designed for bioprocessing such as SOURCE, Sepharose High
Performance, Sepharose Fast Flow, Capto, or Sepharose Big Beads.
See Appendix 3 for column selection and packing.
Equipment selection
Appendix 4 provides a guide to the selection of systems for IEX.
Care of IEX media

When IEX media have been in use for some time, it might become necessary to remove
precipitated proteins or other contaminants that have built up in the column. The need
for cleaning can be seen by the appearance of a colored band at top of the column, a space
between the upper adapter and the bed surface, a loss in resolution, or a significant increase
in back pressure. A general cleaning procedure for each IEX medium is given in Chapter 3 and
Appendix 10 also contains recommended procedures for severe contamination by precipitated
proteins, lipids, hydrophobically bound proteins, or lipoproteins. In all cases, prevention is better
than cure and routine cleaning is recommended.
Always use filtered buffers and samples to reduce the need for additional column
maintenance. See Appendix 1 for further details on sample preparation.
Always degas buffers and keep buffers, columns and samples at the same temperature
to avoid the formation of air bubbles in the column.
46 11000421 AC
Filter cleaning solutions before use and always re-equilibrate the column with start
buffer before the next separation.
If an increase in back pressure is observed, either on the pressure monitor or by seeing
the surface of the medium move downwards, check that the problem is actually caused
by the column before starting the cleaning procedure. Disconnect one piece of equipment
at a time (starting at the fraction collector), start the pump, and check the pressure
after each piece is disconnected. A dirty on-line filter is a common cause of increased
back pressure. Check back pressure at the same stage during each run, since the value
can vary within a run during sample injection or when changing to a different buffer.
Troubleshooting
The desired IEX separation: target proteins well-resolved by gradient elution
equilibration
sample
injection
volume
gradient
elution
regeneration
high salt wash
1M
NaCl concentration
re-equilibration
5 CV
tightly bound
molecules
elute in high
salt wash
10 to 20 CV
5 to 10 CV
5 to 10 CV
Column volumes (CV)
If only certain peaks are of interest in this well-resolved, gradient-elution separation, it can be
advantageous to transfer to a step elution in order to save time and buffer. The rest of this section
focuses on practical problems that might lead to a suboptimal IEX separation.
Sample elutes before salt gradient begins

high salt wash
5 to 10 CV
NaCl concentration
1M
sample
injection
volume
equilibration
5 to 10 CV
re-equilibration
5 to 10 CV
Column volumes (CV)
Ensure that buffers are in the correct containers. Reduce ionic strength of sample by desalting
(see Buffer exchange and desalting in Appendix 1), or dilution with start buffer. For an anion
exchanger, increase buffer pH, for a cation exchanger, decrease buffer pH. If proteins still do
not bind at any pH, the column might be contaminated by detergent.
11000421 AC 47
Sample still eluting when gradient begins

high salt wash
5 to 10 CV
NaCl concentration
1M
sample
injection
volume
equilibration
5 to 10 CV
re-equilibration
5 to 10 CV
Column volumes (CV)
After sample application the UV trace must return to baseline before elution begins, otherwise proteins
that do not bind to the column interfere with the separation. Increase the volume of start buffer
(equilibration step) before starting the gradient elution.
Sample elutes during high salt wash

high salt wash
5 to 10 CV
NaCl concentration
1M
sample
injection
volume
equilibration
5 to 10 CV
re-equilibration
5 to 10 CV
Column volumes (CV)
Proteins are binding too strongly. Ensure that buffers are in the correct containers. If using an
anion exchanger, decrease buffer pH, if using a cation exchanger, increase buffer pH.
Protein(s) of interest eluting late in gradient

Proteins are binding too strongly. Increase ionic strength of gradient. It is preferable to alter pH
if a very high salt concentration is required for elution. For an anion exchanger, decrease buffer
pH and for a cation exchanger, increase buffer pH. Refer also to Table 2.4.
Protein(s) of interest eluting too early in gradient

Proteins are not binding strongly. Check ionic strength of gradient. Alter pH, for an anion exchanger,
increase buffer pH and for a cation exchanger, decrease buffer pH. Refer also to Table 2.4.
Proteins(s) of interest not sufficiently resolved

Refer to the contents of this chapter to review key parameters for improving resolution.
Refer also to Table 2.4.
48 11000421 AC
Table 2.4. Troubleshooting

Situation
Cause
Remedy
Reduced or no flow
through the column
Outlet closed or pumps not

working
Open outlet. Check pumps for signs of leakage

(if using a peristaltic pump, check tubing also).
Blocked filter, end-piece,

adapter, or tubing.
Remove and clean or replace if possible.

Always filter samples before use.
Lipoproteins or protein
aggregates have
precipitated.
Remove lipoproteins and aggregates during sample

preparation, see Appendix 1.
Follow cleaning procedures, see Appendix 10.
Protein precipitation in
the column.
Modify buffer, pH and/or salt conditions during

the run to maintain stability.
Protein precipitation in the

column caused by removal
of stabilizing agents during
separation.
Modify start buffer and elution buffer to maintain

stability.
Microbial growth has

occurred in the column.
Store in the presence of 20% ethanol1 to prevent

microbial growth when not in use.
Always filter buffers.
Sample applied incorrectly.
Check bed surface and top filter for possible

contamination.
Large mixing spaces at top

of or after column.
Adjust top adapter to surface of medium if necessary.

Reduce all post-column volumes.
Incorrect buffer pH and/or

ionic strength.
Check pH and ionic strength to ensure that column

was re-equilibrated after previous run. Check
conditions required. Prepare new solutions.
Peak of interest is poorly

resolved from other major
peaks.
Suboptimal elution conditions, Alter elution conditions: alter pH, use shallower
e.g., incorrect pH, gradient
gradient, reduce flow rate (listed in priority order).
too steep, flow rate too high.
Proteins do not bind

or elute as expected.
Sample is too viscous.
Dilute with buffer. Maintain protein concentration

below 50 mg/ml.
Column is poorly packed.
Check column efficiency, see Appendix 3.

Repack if needed. Use prepacked columns.
Column overloaded.
Decrease sample load.
Lipoproteins or protein
aggregates have
precipitated.
Remove lipoproteins and aggregates during sample

preparation (see Appendix 1).
Precipitation of proteins in
the column.
Modify buffer, pH and/or salt conditions during the

run to maintain stability.

Store in the presence of 20% ethanol1 to prevent

microbial growth. Always filter buffers.
Proteins or lipids have

precipitated on the column
or column filter.
Clean the column and exchange or clean the filter.

Check pH and salt stability of sample.
Sample not filtered properly.
Clean the column, filter the sample and repeat.
Sample has changed during

storage.
Prepare fresh samples.
Protein might be unstable or Determine the pH and salt stability of the protein.
inactive in the elution buffer.
Column equilibration
incomplete.
Repeat or prolong the equilibration step until

conductivity and pH are constant.
Continues on following page

11000421 AC 49
Table 2.4 cont.
Situation
Protein elutes later than

expected or not at all.
Protein elutes earlier than

expected (during the wash
phase)
Leading or very rounded

peaks in chromatogram.
Peaks are tailing.
Cause
Remedy
Incorrect buffer pH and/or

ionic strength.
Check conditions required. Prepare new solutions.
Proteins are forming

aggregates and binding
strongly to the medium.
Use urea or zwitterions, betaine up to 10%, taurine

up to 4%.
Sample or buffer conditions

are different from previous
runs.
Check sample and buffer conditions.

Store in the presence of 20% ethanol to prevent

microbial growth when not in use. Always filter
buffers. Follow cleaning procedures, see Appendix 10.
Incorrect buffer pH.
Check pH meter calibration. Use a buffer pH closer to

the pI of the protein.
Ionic strength too low.
Increase salt concentration in elution buffer.
Ionic interactions between

protein and matrix.
Maintain ionic strength of buffers above 50 mM.
Hydrophobic interactions
between protein and matrix.
Reduce salt concentration to minimize hydrophobic

interaction. Increase pH. Add suitable detergent or
organic solvent, e.g., 5% isopropanol.
Ionic strength of sample or

buffer is too high.
Decrease ionic strength of sample or buffer.
Incorrect pH conditions.
Increase pH (anion exchanger). Decrease pH (cation

exchanger).
Column equilibration
incomplete.
Repeat or prolong the equilibration step until

conductivity and pH are constant.
Channeling in the column.
Repack column using a thinner slurry of medium.

Check column packing (see Appendix 3).
Column overloaded.
Decrease sample load and repeat.
Column contaminated.
Clean using recommended procedures.
Incorrect start buffer

conditions, sample is not
binding to column.
Adjust pH. Check salt concentration in start buffer.
Sample too viscous.
Dilute in application buffer.
Column packing too loose.
Check column efficiency (see Appendix 3). Repack

using a higher flow rate. Use prepacked columns.
Peaks have a leading edge.
Column packing compressed. Check column efficiency (see Appendix 3). Repack
using a lower flow rate. Use prepacked columns.
Medium/beads appears
in eluent.
Column packing compressed. Check column efficiency (see Appendix 3). Repack
using a slower flow rate. Use prepacked columns.
Bed support end piece is
loose or broken.
Replace or tighten.
Column operated at too high Do not exceed recommended operating pressure for
pressure.
medium or column.
Low recovery of activity, but

normal recovery of protein.

50 11000421 AC
Medium has been damaged

during column packing.
Do not use magnetic stirrers when equilibrating

loose IEX medium
Protein might be unstable or

inactive in the buffer.
Determine the pH and salt stability of the protein.
Enzyme separated from

cofactor or similar.
Test by pooling aliquots from the fractions and

repeating the assay.
Table 2.4 cont.
Situation
Cause
Remedy
Protein yield lower than

expected.
Protein might have been

degraded by proteases.
Add protease inhibitors to the sample and buffers to

prevent proteolytic digestion. Run sample through a
medium such as Benzamidine Sepharose 4 Fast Flow
(high sub) to remove trypsin-like serine proteases.
Adsorption to filter during

sample preparation.
Use another type of filter.
Sample precipitates.
Check pH and salt conditions, adjust to improve

sample solubility.
Hydrophobic proteins.
Add denaturing agents, polarity reducing agents or

detergents. Add 10% ethylene glycol to running buffer
to prevent hydrophobic interactions.
Nonspecific adsorption.
Reduce salt concentration to minimize hydrophobic

interaction. Add suitable detergent or organic solvent,
e.g., 5% isopropanol1. If necessary, add 10% ethylene
glycol to running buffer to prevent hydrophobic
interactions.
Sample absorbs poorly at

chosen wavelength.
If appropriate, check absorbance range on monitor.

If satisfactory, use a different wavelength, e.g.,
214 nm instead of 280 nm.
Different assay conditions

have been used before and
after the chromatographic
step.
Use same assay conditions for all assays.
Excessive band broadening.
Check column packing. Repack if necessary.
Peaks too small.
More sample is recovered

than expected.
Protein co-eluting with other Optimize conditions to improve resolution.

substances.
Check buffer conditions used for assay before and
after the run. Check selection of medium.
More activity is recovered

than was applied to the
column.
Different assay conditions

have been used before and
after the chromatography
step.
Use same assay conditions for all assays.
Removal of inhibitors during

separation.
Back pressure increases
during a run or during
successive runs.
Bed compressed.
If possible repack the column or use a new column.

Check sample preparation.
Microbial growth.
Store in the presence of 20% ethanol to prevent

microbial growth. Always filter buffers. Follow
cleaning procedures, see Appendix 10.
Turbid sample.
Improve sample preparation (see Appendix 1).

Improve sample solubility: add betaine (max. 10% w/v
at 25C), taurine (max. 4% w/v at 25C, below pH 8.5)
or glycerol (1% to 2 %). For hydrophobic samples, add
ethylene glycol, urea, detergents, or organic solvents.
Precipitation of protein in the Clean using recommended methods. If possible,

column filter and/or at the
exchange or clean filter or use a new column. Include
top of the bed.
any additives that were used for initial sample
solubilization in the running buffer.
Incorrect pH is causing
precipitation.
Calibrate pH meter, prepare new solutions and try

again. Change pH.
Precipitation of lipoproteins
at increased ionic strength.
Lipoproteins are removed prior to chromatography by

the addition of 10% dextran sulfate (final 0.2%), and
1 M calcium chloride (final 0.5 M).
11000421 AC 51
Table 2.4 cont.
Situation
Cause
Remedy
Air bubbles in the bed.
Buffers not properly

degassed.
Degas buffers thoroughly.
Column packed or stored at

cool temperature and then
warmed up.
Remove small bubbles by passing degassed buffer

through the column; take special care if buffers are
used after storage in a fridge or cold room.
Do not allow column to warm in sunlight or
heating system.
Repack column if possible (see Appendix 3).
Cracks in the bed.
Large air leak in column.
Check all connections for leaks.

Repack the column if possible (see Appendix 3).
Negative peaks at solvent

front.
Refractive index effects.
Exchange the sample into start buffer.
Unexpected peaks in
chromatogram.
Buffer impurities.
Clean the buffer by running it through a precolumn.

Use high quality reagents.
Peaks appear on gradients.
Incomplete elution of
previous sample.
Wash the column according to recommended

blank methods.
Spikes in chromatogram.
Air bubble trapped in UV

monitor flow cell.
Always use degassed buffers.
UV baseline rises with

gradient.
Micelle formation as salt

concentration changes.
Work below or above the critical micelle

concentration of any detergents being used or change
the gradient so that the increase in UV absorption
does not occur while the samples are eluting.
Buffer impurities.
Use high quality reagents.
52 11000421 AC
Chapter 3
Ion exchange chromatography media
Introduction
Historically, several different types of material have been used as a base matrix to which
positively or negatively charged groups are covalently attached to form an IEX medium. Chapter
1 describes how the matrix characteristics determine chromatographic properties such as
efficiency, capacity, and recovery as well as chemical and physical stability and flow properties.
IEX media such as Sepharose High Performance, Sepharose 6 Fast Flow, SOURCE, and Capto
have much improved flow properties compared to earlier media and show no change in bed
volume under conditions of changing ionic strength or pH. Stringent conditions can be used for
cleaning the media when required and there is no need for frequent column repacking. Most
of these media are also designed to meet the throughput and cleaning-in-place requirements
for large-scale industrial chromatography. The following descriptions of different IEX media
will start from high-resolution media for purification and analysis in small scale, continue with
media for many standard applications, and end up with media for larger scales.
MiniBeads: purification or analysis of microgram to milligram

quantities with high resolution
Use MiniBeads for polishing steps at microscale when high resolution is essential and
the capacity of the prepacked column is sufficient.
Use MiniBeads for intermediate purification if only microgram to milligram quantities
are required, if there is no requirement for scale-up, and if the capacity of the prepacked
column is sufficient. To avoid column blockage, it is especially important to remove
particulate matter before using MiniBeads.
Use MiniBeads for faster, higher resolution separations compared to MonoBeads, if the
capacity of the prepacked column is sufficient.
Run MiniBeads on systems KTA chromatography systems such as KTA pure 25 and
HPLC systems. HPLC systems are recommended for optimal performance of the smallest
columns (PC 3.2/3). Appendix 4 provides guidance on selecting the right KTA system.
MiniBeads are based on a nonporous, monodispersed matrix of rigid, hydrophilic polymer
particles, substituted with quaternary amino (Q) or methyl sulfonate (S) groups. The very small
size (3 m), uniformity and physical rigidity of the particles create excellent conditions for
extremely high-resolution ion exchange separations at relatively high flow rates and low back
pressures (nonuniform, porous particles would create higher back pressures, reduce flow rate
and impair achievable resolution). Such high resolution is essential for successful separation of
complex samples in the picogram (pg) to microgram (g) scale. The strong ion exchange groups
(Q and S) maintain their charge over a broad pH range, allowing selection of the most suitable
pH for each application.
Media characteristics
Composition: rigid, nonporous matrix of monodisperse, hydrophilic polymer particles (3 m)
substituted with quaternary amino (Q) or methyl sulfonate (S) groups (Table 3.1).
11000421 AC 53
Table 3.1. Characteristics of MiniBeads media

Product
Functional group
pH stability1
Mean particle size
-CH2-N+-(CH3)3
Long term: 3 to 11
Short term: 1 to 14
3 m (monosized)
-CH2-SO3-
Long term: 3 to 11
Short term: 1 to 14
3 m (monosized)
Strong anion exchanger

Mini Q
Strong cation exchanger
Mini S
1
Long-term pH stability refers to the pH interval where the medium is stable over a long period of time without adverse
side effects on the chromatography performance. Short-term pH stability refers to the pH interval for regeneration,
cleaning-in-place, and sanitization procedures. All ranges are estimates based on experience and knowledge gained at GE.
Purification options
Mini Q and Mini S media are available prepacked in Precision (PC 3.2/3) and Tricorn (4.6/50 PE)
columns for high-resolution purification of biomolecules (Fig 3.1). The purification options for
the prepacked columns are shown in Table 3.2.
Fig 3.1. Mini Q and Mini S media are available prepacked in Precision (PC 3.2/3) and Tricorn (4.6/50 PE) columns.
Table 3.2. Purification options for Mini Q and Mini S prepacked columns
Product, column
volume
Binding capacity
per column
Recommended
Maximum working flow
flow rate rate range
Working
(ml/min)
(ml/min)
pH range1
Maximum
operating back
pressure2
(MPa/psi)
1 MPa = 10 bar
Strong anion exchangers

Mini Q PC 3.2/3, 0.24 ml3 1.44 mg (a-amylase, 1.0
Mr 49 000)
1.44 mg (trypsin
inhibitor, Mr 20 100)
0.1 to 1.0
3 to 11
10/1450
2.0
0.5 to 2.0
3 to 11
18/2600
Mini S PC 3.2/3, 0.24 ml3
1.2 mg (ribonuclease, 1.0

Mr 13 700)
1.2 mg (lysozyme,
Mr 14 300)
0.1 to 1.0
3 to 11
10/1450
Mini S 4.6/50 PE, 0.8 ml
4 mg (ribonuclease,
Mr 13 700)
4 mg (lysozyme,
Mr 14 300)
2.0
0.5 to 2.0
3 to 11
18/2600
Mini Q 4.6/50 PE, 0.8 ml
4.8 mg (a-amylase,
Mr 49 000)
4.8 mg (trypsin
inhibitor, Mr 20 100)
Strong cation exchangers
1
2
3
Working pH range refers to the pH interval where the medium can be operated as intended without adverse long-term effects.
Maximum operating back pressure refers to the pressure above which the medium begins to compress.
Requires a Precision Column Holder for attachment to HPLC systems, see Appendix 4.
54 11000421 AC
Purification examples
Fast separations at high resolution
100
Column:
Sample:
Elution buffer (%)
A 280 nm
0.0030
0.0020
0.0010
0.0
15.0
0.0000
0.0
5.0
Sample volume:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
Mini S 4.6/50 PE
a-chymotrypsinogen A (25 g/ml)
ribonuclease A (75 g/ml)
lysozyme (25 g/ml)
200 l
20 mM sodium acetate, pH 5.0
20 mM sodium acetate, 400 mM NaCl, pH 5.0
0.83 ml/min
0% to 100% elution buffer in 12 CV
10.0
Time (min)
Fig 3.2. Separation of a protein mixture on Mini S 4.6/50.

100
0.25
Elution buffer (%)
A 280 nm
0.20
0.15
0.10
Column:
Sample:
Mini S PC 3.2/3
a-chymotrypsinogen A, ribonuclease A,
cytochrome C, lysozyme (6:10:6:5), 25 g/ml
Sample load:
6 g
Start buffer:
20 mM acetic acid, pH 5.0
Elution buffer:
20 mM acetic acid, 500 mM lithium chloride, pH 5.0
Flow rate (velocity): 0.80 ml/min (10 cm/min)
Gradient:
0% to 100% elution buffer in 6 min (20 CV)
0.05
0.00
0.0
0.0
Time (min)
5.0
Fig 3.3. Mini S PC 3.2/3 gives fast, high-resolution separation.
Purity check
Column:
Start buffer:
Elution buffer:
Flow rate:
Mini Q 4.6/50 PE
10 mM NaOH
10 mM NaOH, 2 M NaCl
1.0 ml/min
Biotinylated 20-mer
0.0
A 260 nm
Crude
synthesis
mixture
20.0
50.0
Conductivity (mS/cm)
20.0
40.0
50.0
A 260 nm
40.0
After
purification
0.0
0.0
20.0
30.0
Volume (ml)
40.0
0.0
20.0
30.0
40.0
Volume (ml)
Fig 3.4. Purity check of 5-biotinylated synthetic oligonucleotide 20-mer on Mini Q 4.6/50 PE before and
after purification on a RESOURCE RPC column.
11000421 AC 55
Long-term reproducibility
Column:
Sample:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
Injection
A 280 nm
Mini S PC 3.2/3
Chymotrypsinogen A, ribonuclease A,
lysozyme, 6 mg in ratio 1:3:1
20 mM acetic acid, pH 5.0
20 mM acetic acid, 400 mM NaCl, pH 5.0
0.4 ml/min
0% to 100% elution buffer in 12 min (20 CV)
51
201
5.0
10.0
15.0
Time (min)
Fig 3.5. Chromatograms from the first, 51st, and 201st separation of a series run on the same Mini S PC 3.2/3
column. The same consistent reproducibility has been confirmed on Mini Q PC 3.2/3 (data not shown).
Performing a separation
Guidelines for selection of media, buffer, pH, and ionic strength conditions and method
optimization are given in Chapter 2. Use the instructions given here as a basis from which to
optimize a separation.
and avoid any deterioration in column performance, especially when using small
particles such as MiniBeads. Samples must be fully dissolved and free from particles or
other material likely to interfere with the separation. Refer to Chapter 2 and Appendix 1
for recommendations and advice on sample preparation.
and chemicals. Filter solutions through 0.22 m filters. To avoid formation of air bubbles
in a packed column, ensure that column and buffers are at the same temperature when
The pH of the start buffer should be at least 0.5 to 1.0 pH unit above the pI of the target
substance when using an anion exchanger (Q) and 0.5 to 1.0 pH unit below the pI of the target
substance when using a cation exchanger (S). See Appendix 2 for recommendations on
volatile and nonvolatile buffer systems for anion and cation exchangers.
For samples with unknown charge properties, try the following:
anion exchange (Q)
start buffer: 20 mM Tris-HCl, pH 8.0
cation exchange (S)
start buffer: 20 mM 2-(N-Morpholino)ethanesulfonic acid (MES), pH 6.0
Users of KTA systems with automatic buffer preparation functionality can select
one of the buffer recipes recommended for anion exchange chromatography at
pH 8.0 or cation exchange chromatography at pH 6.0, see KTA Laboratory-scale
Chromatography Systems: Instrument Management Handbook, 29010831.
56 11000421 AC
First-time use or after long-term storage

1. To remove ethanol, wash with 4 CV of distilled water at 0.1 ml/min (Mini Q and S PC 3.2/3,
0.24 ml columns) or 0.5 ml/min (Mini Q and S 4.6/50 PE, 0.8 ml columns). This step
ensures removal of ethanol and avoids the risk of precipitation if buffer salts were to
come into contact with the ethanol. The step can be omitted if precipitation is not likely
to be a problem.
2. Wash with 4 CV of start buffer at 0.4 ml/min (Mini Q and S PC 3.2/3, 0.24 ml columns) or
0.8 ml/min (Mini Q and S 4.6/50 PE, 0.8 ml columns).
3. Wash with 4 CV of elution buffer, same flow as step 2.
4. Wash with 4 CV of start buffer, same flow as step 2.
Separation by gradient elution

Flow rates: 0.4 ml/min (PC 3.2/3, 0.24 ml columns) or 0.8 ml/min (4.6/50 PE, 0.8 ml columns).
Collect fractions throughout the separation.
3. Wash with 5 to 10 CV of start buffer or until the baseline, eluent pH, and conductivity
are stable, that is, when all unbound material has washed through the column.
4. Begin elution using a gradient volume of 10 to 20 CV and an increasing ionic strength
up to 0.5 M NaCl (50%B).
5. Wash with 5 CV of 1 M NaCl (100%B) to elute any remaining ionically bound material.
6. Re-equilibrate with 5 to 10 CV of start buffer or until eluent pH and conductivity reach
the required values.
Separation by step elution

Although separations by step elution (see Chapter 2) can be performed using MiniBeads,
gradient elution is recommended to maximize resolution.
can be used to remove nonionic detergents. When selecting an organic solvent, check the
chemical stability of the medium to determine a suitable concentration.
Refer to Chapter 2 for advice on optimizing the separation. Check column performance
regularly by determining column efficiency and peak symmetry. See Appendix 3.
Cleaning
Correct preparation of samples and buffers and application of a high salt wash (1 M NaCl) at
the end of each separation should keep most columns in good condition. However, reduced
performance, a slow flow rate, increasing back pressure or complete blockage are all
indications that the medium needs to be cleaned using more stringent procedures in order to
remove contaminants.
Reverse the direction of flow during column cleaning so that contaminants do not need to
pass through the entire length of the column. The number of column volumes and time
required for each cleaning step can vary according to the degree of contamination.
11000421 AC 57
Removing common contaminants

1. Wash with 2 CV of 2 M NaCl at 0.2 ml/min.
2. Wash with 4 CV of 1 M NaOH at 0.2 ml/min.
3. Wash with 2 CV of 2 M NaCl at 0.2 ml/min.
4. Rinse with at least 2 CV of distilled water at 0.2 ml/min until the UV-baseline and eluent
pH are stable.
5. Wash with at least 4 CV of start buffer or storage buffer at 0.2 ml/min until pH and
conductivity values have reached the required values.
To remove precipitated proteins, lipids, hydrophobically bound proteins, or lipoproteins, refer to
Appendix 1.
Chemical stability
For daily use, MiniBeads are stable in all common aqueous buffers in the pH range of 3 to 11
and in the presence of additives such as denaturing agents (8 M urea or 6 M guanidine
hydrochloride), nonionic or ionic detergents, and up to 30% acetonitrile in aqueous buffers. Note
that aqueous solutions of urea, ethylene glycol, and similar compounds will increase the back
pressure due to increased viscosity.
MiniBeads can be used with organic solutions such as dimethylsulfoxide, dimethylformamide,
or formic acid, but the separation properties of the media will change.
Avoid anionic detergents with Mini Q. Avoid cationic detergents with Mini S. Avoid
oxidizing agents.
Storage
For column storage, wash with 4 CV of distilled water followed by 4 CV of 20% ethanol. Degas
the ethanol/water mixture thoroughly and apply at a low flow rate to avoid overpressuring the
column. Store at room temperature or, for long periods, store at 4C to 8C. Whenever possible,
use the storage and shipping device if supplied by the manufacturer. Ensure that the column is
sealed well to avoid drying out. Do not freeze.
58 11000421 AC
MonoBeads: purification of milligram quantities with high resolution

Use MonoBeads for polishing steps at laboratory scale when high resolution is essential
and a higher capacity than MiniBeads is required.
Use MonoBeads for capture or intermediate purification when milligram quantities are
required, when there is no requirement for scale-up, and/or when prepacked MiniBead
columns do not offer sufficient capacity. Note that, to avoid column blockage, it is
especially important to remove particulate matter before using MonoBeads.
Run MonoBeads on KTA chromatography systems and HPLC systems. Appendix 4
provides guidance on selecting the right KTA system. HPLC systems are recommended
for optimal performance of the smallest columns (PC 1.6/5).
Mono Q and Mono S IEX media are based on a hydrophilic matrix made from monodispersed,
rigid, polystyrene/divinyl benzene particles, substituted with quaternary ammonium (Q) or
methyl sulfonate (S) groups (Fig 3.6). This combination confers extreme chemical and physical
stability to the media. The small particle sizes (10 m) allow fast binding and dissociation to
facilitate high resolution while the uniformity of the particles ensures high flow rates at low back
pressures. The strong ion exchange groups (Q and S) maintain their charge over a broad pH range
(Fig 3.7), allowing selection of the most suitable pH for each application.
Fig 3.6. Electron micrograph of MonoBeads showing their distinct monodispersity.

Mono Q
1.0 ml ion exchanger in 1 M KCl
10
10
0.1
0.2
HCl (mmol)
0.3
Mono S
1.0 ml ion exchanger in 1 M KCl
12
pH
pH
12
0.4
0.1
0.2
0.3
0.4
HCl (mmol)
Fig 3.7. Titration curves for Mono Q and Mono S. Binding capacity remains constant over a broad pH
working range.
11000421 AC 59
Composition: rigid, monodisperse, polystyrene/divinyl benzene particles (10 m) with an
optimized pore size distribution. The base matrix is substituted with quaternary amino (Q) or
methyl sulfonate groups (S), see Table 3.3.
Table 3.3. Characteristics of MonoBeads media
Product
Functional group
pH stability1
-CH2-N+-(CH3)3
Long term: 2 to 12
10 (monosized)

Mono Q
Short term: 2 to 12
Mono S
-CH2-SO3-
Long term: 2 to 12
10 (monosized)
Short term: 2 to 14
1
side effects on chromatographic performance. Short-term pH stability refers to the pH interval for regeneration,
MonoBeads (Q and S) are available in convenient prepacked Tricorn PE (PEEK) and Tricorn GL
(glass) columns (Fig 3.8). Purification options for the prepacked columns are described in Table 3.4.
Fig 3.8. MonoBeads (Q and S) are available prepacked in Tricorn PC (Precision Column), PE (PEEK), and
Tricorn GL (glass) columns.
60 11000421 AC
Table 3.4. Purification options for Mono Q and Mono S prepacked columns
Product, column
volume
Binding capacity
per column
Recommended
working flow
rate range
(ml/min)
Maximum
operating
back
pressure2
Maximum
(MPa/psi)
flow rate Working 1 MPa =
(ml/min) pH range1 10 bar

Mono Q PC 1.6/5, 0.1 ml3
2.5 mg (thyroglobulin,
Mr 669 000)
0.01 to 0.4
0.4
2 to 12
5/725
Mono Q 5/50 GL, 1 ml
25 mg (thyroglobulin,
Mr 669 000)
65 mg (HSA, Mr 68 000)
80 mg (a-lactalbumin,
Mr 14 300)
0.5 to 3.0
3.0
2 to 12
4/580
Mono Q 4.6/100 PE, 1.7 ml 40 mg (thyroglobulin,

Mr 669 000)
110 mg (HSA, Mr 68 000)
Mr 14 300)
0.5 to 3.0
3.0
2 to 12
4/580
Mono Q 10/100 GL, 8 ml
200 mg (thyroglobulin, 2.0 to 6.0

Mr 669 000)
520 mg (HSA, Mr 68 000)
Mr 14 300)
10.0
2 to 12
4/580
Mono Q HR 16/10, 20 ml
500 mg (thyroglobulin, up to 10.0

Mr 669 000)
1300 mg (HSA, Mr 68 000)
Mr 14 300)
10.0
2 to 12
3/435
Mono S PC 1.6/5, 0.1 ml3
7.5 mg (human IgG,

Mr 160 000)
0.01 to 0.4
0.4
2 to 12
5/725
Mono S 5/50 GL, 1 ml
75 mg (human IgG,
Mr 160 000)
75 mg (ribonuclease,
Mr 13 700)
0.5 to 3.0
3.0
2 to 12
4/580
Mono S 4.6/100 PE, 1.7 ml 130 mg (human IgG,

Mr 160 000)
Mr 13 700)
0.5 to 3.0
3.0
2 to 12
4/580
Mono S 10/100 GL, 8 ml
600 mg (human IgG,

Mr 160 000)
Mr 13 700)
2.0 to 6.0
10.0
2 to 12
4/580
Mono S HR 16/10, 20 ml
1500 mg (human IgG,

up to 10.0
Mr 160 000)
Mr 13 700)
10.0
2 to 12
3/435
1
2
3
Requires a Precision Column Holder for attachment to HPLC systems.
11000421 AC 61
Two-step purification using complementary selectivities
Column:
Sample:
Mono Q HR 5/5
500 ml of T. reesei crude cellulases
in start buffer, 2.5 mg
Start buffer: 20 mM Tris-HCl, pH 7.6
Elution buffer: 20 mM Tris-HCl, 500 mM NaCl, pH 7.6
Flow rate:
1.0 ml/min
Gradient:
0% elution buffer (4 CV), 0% to 40% elution buffer
(21 CV), 40% to 100% elution buffer (15 CV)
Column:
Sample:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
Mono S HR 5/5
Peak 3 from Mono Q HR 5/5
20 mM acetate, pH 3.6
20 mM acetate, 200 mM NaCl, pH 3.6
1.0 ml/min
0% to 100% elution buffer (26 CV)
0.5
A 280 nm
A 280 nm
0.5
10
20
Time (min)
20
10
Time (min)
30
Fig 3.9. Purification of cellulose on Mono Q and Mono S HR 5/5 columns (now available as Mono Q 5/50 GL
and Mono S 5/50 GL).
High-resolution polishing step

Column:
Sample:
Sample load:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
Mono S 5/50 GL
Recombinant transposase TniA partially purified on SOURCE 15Q 4.6/100 PE and HiTrap Heparin HP, 5 ml
14.5 ml
20 mM MES, 1 mM EDTA, 2 mM MgCl2, 1 mM DTT, pH 6.5
20 mM MES, 1 mM EDTA, 2 mM MgCl2, 1 mM DTT, 1 M NaCl, pH 6.5
1 ml/min
(A)
(B)
100
1200
TniA
A 280 nm
Elution buffer (%)
1000
800
600
400
200
Pool
0
0.0
10
20
Volume (ml)
30
40
1 2
3 4 5
Mr
97 000
66 000
45 000
30 000
Lane 1. Sample, clarified extract

diluted five-fold
Lane 2. Pooled from
SOURCE 15Q 4.6/100 PE
Lane 3. Pooled from HiTrap Heparin HP
Lane 4. Pooled from Mono S 5/50 GL
Lane 5. LMW-SDS Marker Kit
Fig 3.10. Final polishing step in purification of a DNA-binding protein, transposase TniA. Two well-resolved
peaks after separation on Mono S 5/50 GL. (A) SDS-PAGE analysis shows fractions from each of the
three steps used in this protocol. (B) PhastSystem electrophoresis unit using SDS-PAGE PhastGel
Homogeneous 12.5 and Coomassie staining.
62 11000421 AC
Sample volume:
Buffer A:
Buffer B:
Gradient:
Column equilibration:
Flow rate:
System:
STI (6 mg/ml)
200 l
200 mM Tris, pH 7.0
Buffer A + 500 mM NaCl
Linear, 0% to 100% B in 20 CV
5 CV
1.0 ml/min
KTA system
Long-term reproducibility
Column:
Sample:
Mono Q 5/50 GL (Tricorn)

Conalbumin (3.0 mg/ml), -lactalbumin (4 mg/ml),
STI (6 mg/ml)
Sample volume:
200 l
Buffer A:
200 mM Tris, pH 7.0
Buffer B:
Buffer A + 500 mM NaCl
Gradient:
Linear, 0% to 100% B in 20 CV
Column equilibration: 5 CV
Flow rate:
1.0 ml/min
System:
KTA system
A280 (mAU)
Injection 2000
Injection 1000
Injection 1
10
15
20
25
Volume (ml)
Fig 3.11. Chromatograms illustrating run to run reproducibility for Mono Q 5/50 GL (Tricorn column).
Runs 1, 1000, and 2000 are shown.
Separation in organic solvents

Column:
Sample:
Sample load:
Start buffer:
A 280 nm
Mono S HR 5/5
Bacitracin 4 mg/ml in start buffer
200 l
90% methanol, 50 mM formic acid/lithium hydroxide (LiOH),
pH 3.8
Elution buffer: 90% methanol,
50 mM formic acid/LiOH, 350 mM lithium perchlorate (LiClO 4),
pH 3.8
Flow rate:
1 ml/min
Gradient:
Time
Fig 3.12. Separation of the peptide bacitracin on Mono S HR 5/5 (now available as Mono S 5/50 GL).
Guidelines for selection of media, buffer, pH, and ionic strength conditions and method optimization
are given in Chapter 2. Use these instructions as a basis from which to optimize a separation.
Correct sample and buffer preparation is essential to achieve optimal separation and to
avoid any deterioration in column performance, especially when using small particles
such as MonoBeads. Samples must be fully dissolved and free from particles or other
material likely to interfere with the separation. Refer to Chapter 2 and Appendix 1 for
recommendations and advice on sample preparation.
and chemicals. Filter solutions through 0.22 m filters. To avoid formation of air bubbles
in a packed column, ensure that column and buffers are at the same temperature when
substance when using an anion exchanger (Q) and 0.5 to 1.0 pH unit below the pI of the target
substance when using a cation exchanger (S). See Appendix 2 for recommendations on
volatile and nonvolatile buffer systems for anion and cation exchangers.
11000421 AC 63

anion exchange (Q)
cation exchange (S)

1. To remove ethanol, wash with 5 CV of distilled water at 0.1 ml/min (PC 1.6/5, 0.1 ml
columns), 1 ml/min (5/50 GL, 1 ml and 4.6/100 PE, 1.7 ml columns), 2 ml/min (10/100 GL,
8 ml columns) or 4 ml/min (HR 16/10, 20 ml columns). This step ensures removal of
ethanol and avoids the risk of precipitation if buffer salts were to come into contact
with the ethanol. The step can be omitted if precipitation is not likely to be a problem.
2. Wash with 5 CV of start buffer at 0.1 ml/min (PC 1.6/5, 0.1 ml columns), 2 ml/min
(5/50 GL, 1 ml and 4.6/100 PE, 1.7 ml columns), 4 ml/min (10/100 GL, 8 ml columns), or
8 ml/min (HR 16/10, 20 ml columns).

Flow rates: 0.1 ml/min (PC 1.6/5, 0.1 ml columns), 2 ml/min (5/50 GL, 1 ml and 4.6/100 PE,
1.7 ml columns), 4 ml/min (10/100 GL, 8 ml columns) or 8 ml/min (HR 16/10, 20 ml columns).

Although separations by step elution (see Chapter 1) can be performed using MonoBeads,
gradient elution is recommended in order to achieve the highest possible resolution.
steps. Do not exceed the maximum recommended flow for the column.
UV baseline, eluent pH and/or conductivity are stable. Organic solvents such as ethanol
can be used to remove nonionic detergents. When selecting an organic solvent, check
the chemical stability of the medium to determine a suitable concentration.
64 11000421 AC

symmetry. See Appendix 3. Refer to Chapter 2 for advice on optimizing the separation.
Cleaning
Correct preparation of samples and buffers and application of a high salt wash (1 M NaCl) at the
end of each separation should keep most columns in good condition. However, reduced
performance, a slow flow rate, increasing back pressure, or complete blockage are all indications
that the medium needs to be cleaned using more stringent procedures to remove contaminants.
Reverse the direction of flow during column cleaning so that contaminants do not need to
pass through the entire length of the column. The number of column volumes and time
required for each cleaning step may vary according to the degree of contamination.
If the cleaning procedure to remove common contaminants does not restore column
performance, change the top filter before trying alternative cleaning methods. Care
should be taken when changing a filter as this can affect the column packing and
interfere with performance.

Flow rates: 0.05 ml/min (PC 1.6/5, 0.1 ml columns), 0.5 ml/min (5/50 GL, 1 ml columns),
0.2 ml/min (4.6/100 PE, 1.7 ml columns), 2 ml/min (10/100 GL, 8 ml columns), or 5 ml/min
(HR 16/10, 20 ml columns).
1. Wash with at least 2 CV of 2 M NaCl.
2. Wash with at least 4 CV of 1 M NaOH.
4. Rinse with at least 2 CV of distilled water until the UV-baseline and the eluent pH are stable.
5. Wash with at least 4 CV of start buffer or storage buffer until pH and conductivity
values have reached the required values.
Appendix 1.
Chemical stability
For daily use, MonoBeads are stable in all common, aqueous buffers in the pH range 2 to 12,
and in the presence of additives such as denaturing agents (8 M urea or 6 M guanidine
hydrochloride), nonionic or ionic detergents, and up to 20% acetonitrile in aqueous buffers. Note
that aqueous solutions of urea, ethylene glycol and similar compounds will increase the back
pressure due to increased viscosity.
MonoBeads can be used with organic solutions such as dimethylsulfoxide, dimethylformamide,
or formic acid, but the separation properties of the media will change.
Avoid anionic detergents with Mono Q. Avoid cationic detergents with Mono S. Avoid
oxidizing agents.
Storage
For column storage, wash with 5 CV of distilled water followed by 5 CV of 20% ethanol. Degas
the ethanol/water mixture thoroughly and apply at a low flow rate to avoid overpressuring
the column. Store at room temperature or, for long periods, store at 4C to 8C. Ensure that the
column is sealed well to avoid drying out. Whenever possible, use the storage and shipping
device if supplied by the manufacturer. Do not freeze.
11000421 AC 65
SOURCE: high-throughput, high-resolution purification, and easy scale-up

Use SOURCE 15 for intermediate purification or polishing steps in laboratory- or
large-scale applications that require high resolution and high throughput (flow
velocities up to 1800 cm/h).
Use SOURCE 30 as an alternative to SOURCE 15 for intermediate purification or polishing
steps in large-scale applications where speed rather than resolution is a priority (flow
velocities up to 2000 cm/h).
Use SOURCE 30 as an alternative to SOURCE 15 for large sample volumes where speed
rather than resolution is a priority. The larger particle size slightly reduces resolution,
but separations can be performed at higher flow rates.
Run SOURCE columns on KTA chromatography systems, HPLC systems, or systems
using peristaltic pumps. Appendix 4 provides guidance on selecting the right KTA system.
SOURCE media are based on a hydrophilic matrix made from monodispersed, rigid,
polystyrene/divinyl benzene and substituted with quaternary ammonium (Q) or methyl
sulfonate (S) groups (Figure 3.13). This combination confers extreme chemical and physical
stability to the media. The small particle sizes allow fast binding and dissociation to facilitate
high resolution while the uniformity and stability of the particles ensures high flow rates at low
back pressure. The strong ion exchange groups (Q and S) maintain their charge over a broad
pH range, allowing selection of the most suitable pH for each application. The high flow rates
that can be used with SOURCE media are more likely to be limited by the equipment available
rather than the physical properties of the media.
Separation methods can be easily scaled up from columns such as RESOURCE Q or S, 1 ml
prepacked with SOURCE 15, to large-scale columns such as FineLINE.
Fig 3.13. Uniform size distribution of SOURCE monodispersed particles.
Composition: rigid, monodisperse, polystyrene/divinyl benzene particles with an optimized
pore-size distribution. The base matrix is substituted with quaternary amino groups (Q) or
methyl sulfonate groups (S), see Table 3.5.
66 11000421 AC
Table 3.5. Characteristics of SOURCE 15 and 30 media

Mean particle size
(m, monosized)
Product
Functional group
pH stability1
SOURCE 15Q
-CH2-N+-(CH3)3
Long term: 2 to 12
Short term: 1 to 14
15
SOURCE 30Q
-CH2-N+-(CH3)3
Long term: 2 to 12
Short term: 1 to 14
30
SOURCE 15S
-CH2-SO3-
Long term: 2 to 13
Short term: 1 to 14
15
SOURCE 30S
-CH2-SO3-
Long term: 2 to 13
Short term: 1 to 14
30
SOURCE Q and S media are available in media packs and in convenient prepacked Tricorn (PE)
and RESOURCE columns (Fig 3.14). Purification options for the media and prepacked columns
are described in Table 3.6.
Fig 3.14. SOURCE is available in media packs and is prepacked in Tricorn and RESOURCE columns.
11000421 AC 67
Table 3.6. Purification options for SOURCE media and prepacked columns
Product, column
volume
Binding capacity per Recommended

column or per ml
working flow
medium
rate range1
Maximum
flow1
Maximum
operating back
pressure3
Working (MPa/psi)
pH range2 1 MPa = 10 bar

SOURCE 15Q
45 mg/ml
(BSA, Mr 67 000)
150 to 900 cm/h
1800 cm/h 2 to 12
0.5/72
SOURCE 30Q
40 mg/ml
(BSA, Mr 67 000)
300 to 1000 cm/h 2000 cm/h 2 to 12
0.5/72
RESOURCE Q, 1 ml
45 mg
(BSA, Mr 67 000)
1.0 to 10 ml/min
10 ml/min
2 to 12
1.5/220
RESOURCE Q, 6 ml
270 mg
(BSA, Mr 67 000)
1.0 to 60 ml/min
60 ml/min
2 to 12
0.6/87
SOURCE 15Q
4.6/100 PE, 1.7 ml
75 mg
(BSA, Mr 67 000)
0.5 to 2.5 ml/min
5 ml/min
2 to 12
4/580

SOURCE 15S
80 mg/ml
150 to 900 cm/h
(lysozyme, Mr 14 500)
1800 cm/h 2 to 13
0.5/72
SOURCE 30S
80 mg/ml
300 to 1000 cm/h 2000 cm/h 2 to 13
0.5/72
RESOURCE S, 1 ml
80 mg
1.0 to 10 ml/min
10 ml/min
2 to 13
1.5/220
RESOURCE S, 6 ml
480 mg
1.0 to 60 ml/min
60 ml/min
2 to 13
0.6/87
SOURCE 15S
4.6/100 PE, 1.7 ml
140 mg
0.5 to 2.5 ml/min
5 ml/min
2 to 13
4/580
1
2
3
See Appendix 5 to convert flow velocity (cm/h) to volumetric flow rate (ml/min) and vice versa.
Use prepacked RESOURCE columns (1 ml or 6 ml) for fast media selection, method
scouting, group separations, sample concentration or clean-up.
Use SOURCE 15Q PE 4.6/100 PE to improve resolution by increasing column length with
further optimization and as the first step towards scaling up.
For column packing in XK columns, see Table 3.7. Select a production column such as FineLINE
for larger volumes.
Table 3.7. Packing of SOURCE 15 and SOURCE 30 chromatography media in XK columns
Volume (ml)
Bed height (cm)
up to 8
up to 10
SOURCE 15
Tricorn 10/100
Tricorn 10/150
up to 12
up to 15
Tricorn 10/200
up to 16
up to 20
up to 30
up to 15
SOURCE 30
XK 16/20
XK 26/20
up to 80
up to 15
XK 26/40
up to 196
> 15
68 11000421 AC
Fast, high-resolution separations
0.10
Elution buffer (%)
A 280 nm
100
0.05
Column:
Sample:
Sample volume:
Start buffer:
Elution buffer:
Flow rate, flow velocity:
Gradient:
RESOURCE Q 1 ml
Pancreatin 5 mg/ml
200 l
20 mM bis-Tris-propane, pH 7.5
20 mM bis-Tris-propane, 500 mM NaCl, pH 7.5
9.6 ml/min, 1800 cm/h
0
0
T ime (min)
Fig 3.15. Separation of pancreatin on RESOURCE Q, 1 ml in 3 min.
100
Elution buffer (%)
A 280 nm
0.05
10
20
Column:
Sample:
Sample volume:
Start buffer:
Elution buffer:
Flow rate, flow velocity:
Gradient:
RESOURCE S 1 ml
Snake venom, 4 mg/ml
100 l
20 mM sodium phosphate, 400 mM NaCl, pH 6.8
1 ml/min, 180 cm/h
30
T ime (min)
Fig 3.16. Separation of snake venom on RESOURCE S, 1 ml at 1 ml/min (180 cm/h).
Scaling up: resolution maintained

Column:
(A) SOURCE 15S, 2.2 ml

(B) SOURCE 15S, FineLINE 100, 390 ml
Ribonuclease, cytochrome C and lysozyme
(A) 0.46 mg in 200 l
(B) 80.5 mg in 350 ml
Start buffer:
Elution buffer:
Flow rates (flow velocities): (A) 2.2 ml/min (300 cm/h)
(B) 385 ml/min (300 cm/h)
Gradient:
0% elution buffer (2 CV)
Sample:
Sample load:
(A)
(B)
100
100
0.05
A 280 nm
0.03
50
0.02
Elution buffer (%)
50
Elution buffer (%)
A 280 nm
0.04
0.01
0
0
10
20
Time (min)
0.00
0
0
20
Time (min)
Fig 3.17. Separation of proteins scaled up from a 2.2 ml column to a 390 ml column.
11000421 AC 69
Figure 3.18 shows an example of SOURCE 30Q used for an intermediate purification step in a
large-scale process. Recombinant P. aeruginosa exotoxin A, produced as a periplasmic protein
in E. coli, was initially purified with STREAMLINE DEAE expanded bed adsorption, followed by
hydrophobic interaction chromatography (HIC) on Phenyl Sepharose 6 Fast Flow (high sub). The
fraction of interest was then further purified on SOURCE 30Q before a final HIC polishing step
on SOURCE 15PHE to remove the final contaminants.
Column:
Sample:
Sample:
Start buffer:
Elution buffer:
Gradient:
SOURCE 30Q, FineLINE 100 (375 ml)

Partially purified recombinant P. aeruginosa exotoxin A, diluted 1:3 with water
1.8 g total protein (0.29 g exotoxin A) in 1.5 l
20 mM sodium phosphate, 1 M NaCl, pH 7.4
785 ml/min (600 cm/h)
0.50
A 280 nm
0.40
0.30
0.20
0.10
Pool
0.00
0
6
8
Volume (l)
10
12
Native PAGE results, Coomassie staining

Lane 1. Pool from step 2 on Phenyl Sepharose
Fast Flow (high sub)
Lane 2. Pool from step 3 on SOURCE 30Q
Lane 3. Pool from step 4 on SOURCE 15PHE
Fig 3.18. Intermediate purification of recombinant Pseudomonas aeruginosa exotoxin A on SOURCE 30Q.
Separations under extreme pH conditions

The high pH stability of SOURCE media makes them well-suited for applications requiring
conditions of extreme pH such as purification of certain peptides and synthetic oligonucleotides, as shown in Figures 3.19 and 3.20.
RESOURCE S, 1 ml
Partially purified bacitracin, 5 mg/ml
100 l
5 mM potassium phosphate, pH 2.8, 30% acetonitrile
5 mM potassium phosphate, 400 mM KCl, pH 2.8, 30% acetonitrile
1 ml/min (180 cm/h)
A 280 nm
Column:
Sample:
Sample volume:
Start buffer:
Elution buffer:
Gradient:
10
T ime (min)
Fig 3.19. Intermediate purification of the peptide bacitracin from Bacillus subtilis on RESOURCE Q, 1 ml.
70 11000421 AC
Method optimization
Sample:
Start buffer:
Elution buffer:
Flow rate:
Crude oligonucleotide 20-mer (10 g)

10 mM NaOH, pH 12
10 mM NaOH, 2 M NaCl, pH 12
1 ml/min
(A)
(B)
(C)
Column: RESOURCE Q, 1 ml
Column: RESOURCE Q, 1 ml
Column: SOURCE 15Q 4.6/100 PE, 1.7 ml
Gradient: 0% to 50% elution buffer in 30 CV Gradient: 20% to 35% elution buffer in 50 CV Gradient: 20% to 35% elution buffer in 50 CV
Conductivity
70
600
Conductivity
100
400
50
200
10
20
Time (min)
30
Conductivity
60
50
40
30
Conductivity
150
A 260 nm
A 260 nm
800
20
40
Time (min)
20
40
60
Time (min)
Fig 3.20. Manipulation of gradient slope and shape to maximize resolution. Initial purification of a 20 mer
oligonucleotide was optimized on RESOURCE Q, 1 ml and transferred to SOURCE Q PE 4.6/100 to further
increase resolution by increasing bed height to 10 cm.
Batch-to-batch reproducibility
Batch-to-batch reproducibility is particularly important for media used for scaling-up and
large scale industrial applications which are under strict regulatory control. Figures 3.21 and 3.22
demonstrate the high batch-to-batch reproducibility of SOURCE 15 and SOURCE 30 media.
SOURCE 30S, 2.2 ml, four separate batches
Chymotrypsinogen, cytochrome C, and lysozyme
0.32 mg/ml bed volume
2.2 ml/min (300 cm/h)
A 280 nm
Columns:
Sample:
Sample load:
Start buffer:
Elution buffer:
Gradient:
10
Time (min)
20
Fig 3.21. Selectivity tests on four production batches of SOURCE 30S.
11000421 AC 71
Columns:
Sample:
Sample volume:
Start buffer:
Elution buffer:
Gradient:
SOURCE 15Q, 2.2 ml, four separate batches

Ovalbumin (3 mg/ml), b-lactoglobulin (3 mg/ml)
200 l
20 mM bis-Tris-propane, pH 7.0
20 mM bis-Tris-propane, 350 mM NaCl, pH 7.0
2.2 ml/min (300 cm/h)
100
0.040
50
Elution buffer (%)
A 280 nm
0.060
0.020
0
0
10
20
Ti me (min)
Fig 3.22. Selectivity tests on four production batches of SOURCE 15Q.
Guidelines for selection of media, buffer, pH and ionic strength conditions, and method
and avoid any deterioration in column performance. Samples must be fully dissolved
and free from particles or other material likely to interfere with the separation. Refer to
Chapter 2 and Appendix 1 for recommendations and advice on sample preparation.
and chemicals. Filter solutions using filters of 0.45 m or 0.22 m for 30 m particles and
0.22 m filters for 15 m particles. To avoid formation of air bubbles in a packed column,
ensure that column and buffers are at the same temperature when preparing for a run.
substance when using an anion exchanger (Q) and 0.5 to 1.0 pH unit below the pI of the
target substance when using a cation exchanger (S). See Appendix 2 for recommendations
on volatile and nonvolatile buffer systems for anion and cation exchangers.
anion exchange (Q)
cation exchange (S)
72 11000421 AC

1. To remove ethanol, wash with 5 CV of distilled water at 2 ml/min (SOURCE 15 4.6/100 PE),
4 ml/min (RESOURCE 1 ml), 6 ml/min (RESOURCE 6 ml), or 200 cm/h for SOURCE packed
in larger columns. This step ensures removal of ethanol and avoids the risk of precipitation
if buffer salts were to come into contact with the ethanol. The step can be omitted if
precipitation is not likely to be a problem.
2. Wash with 5 CV of start buffer, at 2 ml/min (SOURCE 15 4.6/100 PE), 4 ml/min (RESOURCE 1 ml),
6 ml/min (RESOURCE 6 ml), or 200 cm/h for SOURCE packed in larger columns.

Flow rates: 2 ml/min (SOURCE 15 4.6/100 PE), 4 ml/min (RESOURCE 1 ml), 6 ml/min
(RESOURCE 6 ml), or 200 cm/h for SOURCE packed in larger columns.

Flow rates: 2 ml/min (SOURCE 15 4.6/100 PE), 4 ml/min (RESOURCE 1 ml), 6 ml/min
(RESOURCE 6 ml), or 200 cm/h for SOURCE packed in larger columns.
2. Adjust the sample to the chosen starting pH, and ionic strength and apply to the column.
4. Elute the target protein with 5 CV of start buffer containing NaCl at chosen ionic strength.
5. If necessary: repeat step 4 at higher ionic strengths until the target protein(s) has
been eluted.
6. Wash with 5 CV of a high salt solution (1 M NaCl in start buffer) to elute any remaining
ionically bound material.
11000421 AC 73
symmetry. See Appendix 3.
Cleaning
Correct preparation of samples and buffers and application of a high salt wash (1 M NaCl) at the
end of each separation should keep most columns in good condition. However, reduced performance,
a slow flow rate, increasing back pressure or complete blockage are all indications that the medium
needs to be cleaned using more stringent procedures in order to remove contaminants.
Reverse the direction of flow during column cleaning so that contaminatants do
not need to pass through the entire length of the column. The number of column
volumes and time required for each cleaning step varies according to the degree of
contamination. If the cleaning procedure to remove common contaminants does
not restore column performance, change the top filter (when possible) before trying
alternative cleaning methods. Care should be taken when changing a filter as this can
affect the column packing and interfere with performance.

Flow rates: 0.2 ml/min (SOURCE 15 4.6/100 PE), 1 ml/min (RESOURCE 1 ml), 6 ml/min
(RESOURCE 6 ml), or 40 cm/h with a contact time of 1 to 2 h for SOURCE packed in larger columns
5. Wash with at least 4 CV of start buffer or storage buffer until eluent pH and
conductivity have reached the required values.
Appendix 1.
Chemical stability
For daily use, SOURCE media are stable in all common, aqueous buffers pH 2 to 12, denaturing
agents (8 M urea, 6 M guanidine hydrochloride), 75% acetic acid, 1 M NaOH, 1 M HCl, 70%
ethanol, 30% acetonitrile, and with additives such as nonionic detergents.
Avoid cationic detergents with SOURCE S. Avoid anionic detergents with SOURCE Q.
Avoid oxidizing agents.
Storage
For column storage, wash with 5 CV of distilled water followed by 5 CV of 20% ethanol. Include
200 mM sodium acetate in the 20% ethanol solution for SOURCE S. Degas the ethanol/water
mixture thoroughly and apply at a low flow rate to avoid overpressuring the column. Store at
room temperature or, for long periods, store at 4C to 8C. Ensure that the column is sealed well
to avoid drying out. Whenever possible, use the storage and shipping device if supplied by the
manufacturer. Store unused media at 4C to 30C in 20% ethanol. Do not freeze.
74 11000421 AC
Sepharose High Performance: purification with high resolution

Use Sepharose High Performance for intermediate purification steps that require
high capacity and high resolution (flow velocities up to 150 cm/h).
Run Sepharose High Performance columns on KTA chromatography systems.
Appendix 4 provides guidance on selecting the right KTA system.
Sepharose High Performance media are based on a matrix of 34 m particles made from
6% agarose and highly cross-linked for chemical and physical stability. The small particle
size ensures fast binding and dissociation even at high sample loads and flow rates which,
in combination with high selectivity, give high-resolution separations. Particle size and bed
volumes remain stable, despite changes in ionic strength or pH, to ensure fast separations at
high flow rates. The strong ion exchange groups (Q and SP) maintain their charge over a broad
pH range, allowing selection of the most suitable pH for each application.
Composition: sulfopropyl (SP) or quaternary amino (Q) groups coupled to highly cross-linked 6%
agarose via chemically stable ether bonds, see Table 3.8.
Table 3.8. Characteristics of Sepharose High Performance media
Product
Q Sepharose
High Performance
SP Sepharose
High Performance
1
Functional group
-CH2-N+-(CH3)3
-CH2-SO3-
pH stability1
Long term: 2 to 12
Short term: 1 to 14
Long term: 4 to 13
Short term: 3 to 14

34
34
side effects on chromatography performance. Short-term pH stability refers to the pH interval for regeneration,
Sepharose Q and SP High Performance are available in chromatography media packs, in
convenient prepacked HiTrap columns for small-scale work, HiPrep columns for purification
scale-up, and HiScreen columns (Fig 3.23). The purification options for these prepacked formats
are found in Table 3.9.
11000421 AC 75
Fig 3.23. Q and SP Sepharose High Performance media are available prepacked in HiTrap, HiPrep, and
HiScreen columns or in media packs.
Table 3.9. Purification options for Sepharose High Performance media and prepacked columns
Product
Binding capacity per

column or per ml
medium
Recommended Maximum Working Maximum operating

working flow1 flow1
pH range2 back pressure3
(MPa/psi)
1 MPa = 10 bar

Q Sepharose
70 mg/ml
High Performance (HSA, Mr 68 000)
30 to 150 cm/h 150 cm/h 2 to 12
0.5/72
HiTrap Q HP, 1 ml
50 mg (HSA, Mr 68 000) up to 1 ml/min 4 ml/min
2 to 12
0.3/43
HiTrap Q HP, 5 ml
250 mg (HSA, Mr 68 000) up to 5 ml/min 20 ml/min 2 to 12
0.3/43
HiPrep Q HP, 20 ml 1000 mg

(BSA, Mr 68 000)
up to 5 ml/min 20 ml/min 2 to 12
HiScreen Q HP,
4.7 ml
0.6 ml/min
70 mg/ml
(BSA, Mr 68 000)
1.2 ml/min 2 to 12
0.3/43
SP Sepharose
55 mg/ml (ribonuclease, 30 to 150 cm/h 150 cm/h 4 to 13
High Performance Mr 13 700)
0.5/72
HiTrap SP HP, 1 ml 55 mg (ribonuclease,

Mr 13 700)
up to 1 ml/min 4 ml/min
4 to 13
0.3/43
HiTrap SP HP, 5 ml 275 mg (ribonuclease,

Mr 13 700)
0.3/43
HiPrep SP HP 16/10, 1100 mg (ribonuclease, up to 5 ml/min 20 ml/min 4 to 13

20 ml
Mr 13 700)
HiScreen S HP,
4.7 ml
1
2
3
55 mg/ml (ribonuclease, 0.6 ml/min

Mr 13 500)
1.2 ml/min 4 to 12
0.3/43
76 11000421 AC
Use prepacked HiTrap columns (1 ml or 5 ml) for media selection, method scouting,
group separations, small-scale purification, sample concentration, or clean-up. Connect
up to three HiTrap columns in series to scale-up.
Use prepacked HiPrep columns (20 ml) for method development, group separations, larger
scale purification, or sample concentration.
Use prepacked HiScreen columns (4.7 ml, bed height 10 cm) for method development
and screening before scaling up with bed height maintained.
For column packing in Tricorn and XK columns, see Table 3.10.
Table 3.10. Packing volumes and bed heights for Sepharose Q and SP High Performance media packed in
Tricorn and XK columns
Column
Volume (ml)
Bed height (cm)
Tricorn 10/100
up to 8
up to 10
Tricorn 10/150
up to 12
up to 15
Tricorn 10/200
up to 16
up to 20
XK 16/20
up to 30
up to 15
XK 26/20
up to 80
up to 15
XK 26/40
up to 196 ml
> 15 cm
Figure 3.24 shows scaling up from HiTrap SP HP to HiPrep SP HP 16/10. A number of factors
were kept constant, such as sample load/ml medium, flow rates and number of CV in the
gradient. The separation was maintained through a 20-fold scale-up. The scale-up resulted in
similar separation of the sample, which comprised four standard proteins.
HiTrap SP HP, 1 ml
Sample:
HiPrep SP HP 16/10, 20 ml
Sample:
Concanavalin A, ribonuclease A,
a-chymotrypsinogen A, lysozyme,
4 mg protein/ml (3:3:1:1) in start buffer
Sample load:
1 mg protein/ml medium
Sample volume:
5.0 ml, 25% of CV
Flow rate (flow velocity): 2.5 ml/min (75 cm/h)
Start buffer:
50 mM MES, pH 6.0
Elution buffer:
50 mM MES, 1 M NaCl, pH 6.0
Gradient:
0% to 43% elution buffer over 200 ml (10 CV)
Concanavalin A, ribonuclease A,
a-chymotrypsinogen A, lysozyme,
4 mg protein/ml (3:3:1:1) in start buffer
Sample load:
1 mg protein/ml medium
Sample volume:
0.25 ml, 25% of CV
Start buffer:
50 mM MES, pH 6.0
Elution buffer:
Gradient:
0% to 43% elution buffer over 10 ml (10 CV)
0.12
0.12A
0.10
0.10
0.08
280
0.06
0.04
0.02
0
A280
A 280nm
0.14
0.08
0.16
0.14
Conductivity
0.14
0.12
0.12
0.10
0.10
0.08
A280
A 280nm
Conductivity
0.14
A 280nm
A 280nm
0.16
0.06
0.04
0.04
0.04
0.02
0.02
0.02
6 2 8 4 10 6 12 8 14 10 16 12
Volume (ml)
Volume (ml)
14
16
40
Conductivity
A280
0.08
0.06
0
4
Conductivity
0.06
0
80
12040 16080 200120240160280

200 320
240
Volume (ml)
Volume (ml)
280
320
Fig. 3.24. Scaling up the separation of four standard proteins from HiTrap SP to HiPrep SP HP 16/10.
11000421 AC 77
Group separations
Figure 3.25 shows a group separation of human serum proteins on HiTrap Q HP using a onestep elution that had been optimized to ensure that IgG flowed through the column leaving
other serum components to be eluted separately.
Column:
Sample:
HiTrap Q HP 1 ml
Human serum, filtered (0.45 m filter) and
buffer exchanged to start buffer on a PD-10 Desalting column
Sample volume:
1.0 ml
Start buffer:
Elution buffer:
75 mM Tris-HCl, 1.0 M NaCl, pH 8.0
100% elution buffer
1.0
Mr
97 000
66 000
0.8
A 280 nm
pool 1
pool 2
45 000
0.6
30 000
20 100
0.4
14 400
1
0.2
0
0
10
15
20
25
30
35
Volume (ml)
40
Lane 1. Low Molecular Weight (LMW) Calibration Kit,

GE Healthcare
Lane 2. Start material, buffer exchanged
human serum, diluted 1:75
Lane 3. Flowthrough, pool 1, diluted 1:10
Lane 4. Desorbed material, pool 2, diluted 1:25
Fig 3.25. Separation of IgG from human serum proteins on HiTrap Q HP 1 ml, using one-step elution.
Analysis by SDS-PAGE (silver staining).
Concentrating a sample prior to SEC minimizes sample volume and facilitates a rapid, highresolution size separation. HiTrap columns offer a convenient, ready-to-use solution for sample
concentration. Table 3.11 gives examples of the high concentration factors achieved when
concentrating proteins from very dilute starting material using HiTrap columns prepacked with
Sepharose HP medium. Similar results can be achieved with HiTrap columns prepacked with
Sepharose Fast Flow or Sepharose XL media.
Table 3.11. Sample concentration using 1 ml HiTrap ion exchange columns
Column
Sample
HiTrap Q HP, 1 ml
Human IgG
HiTrap SP HP, 5 ml
78 11000421 AC
Lysozyme
Sample
concentration
(g/ml)
Sample
volume
(ml)
Eluted
concentration
(g/ml)
Volume
eluted
(ml)
23
450
3180
3.0
150
92
10
100
4700
2.0
50
93
1010
10
3370
3.0
100
333
150
3170
16.0
100
33
1500
3720
13.2
114
98
Concentration
factor
Yield
(volume)
(%)
Filter buffers after all salts and additives have been included. Use high-quality water
and chemicals. Filter solutions through 0.45 m or 0.22 m filters. To avoid formation
of air bubbles in a packed column, ensure that column and buffers are at the same
temperature when preparing for a run.
substance when using an anion exchanger (Q) and 0.5 to 1.0 pH unit below the pI of the
target substance when using a cation exchanger (S). See Appendix 2 for recommendations
on volatile and nonvolatile buffer systems for anion and cation exchangers.
anion exchange (Q)
cation exchange (S)

1. To remove ethanol, wash with 1 CV of distilled water at 1 ml/min (HiTrap 1 ml), 5 ml/min
(HiTrap 5 ml), 0.6 ml/min (HiScreen 4.7 ml), 0.8 ml/min (HiPrep 20 ml), or at 25 cm/h for
Sepharose High Performance packed in larger columns. This step ensures removal of
ethanol and avoids the risk of precipitation if buffer salts were to come into contact
with the ethanol. The step can be omitted if precipitation is not likely to be a problem.
2. Wash with 5 CV of start buffer at 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml)
0.6 ml/min (HiScreen 4.7 ml), 3 ml/min (HiPrep 20 ml) or at 50 cm/h for Sepharose High
Performance packed in larger columns.
5. Run a blank elution before applying sample.
11000421 AC 79

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 0.6 ml/min (HiScreen 4.7 ml), 3 ml/min
(HiPrep 20 ml), or at 50 to 100 cm/h for Sepharose High Performance packed in larger
columns. Collect fractions throughout the separation.

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiPrep 20 ml), 0.6 ml/min (HiScreen 4.7 ml), or
at 50 to 100 cm/h for Sepharose High Performance packed in larger columns.
conductivityare stable.
3. Wash with 5 to 10 CV of start buffer or until the baseline, eluent pH and conductivity
been eluted.
symmetry. See Appendix 3. Note that this does not apply to HiTrap columns.
Cleaning
performance, a slow flow rate, increasing back pressure or complete blockage are all indicators
that the medium needs to be cleaned using more stringent procedures to remove contaminants.
80 11000421 AC
Reverse the direction of flow during column cleaning so that contaminants do not need
to pass through the entire length of the column. The number of column volumes and
time required for each cleaning step varies according to the degree of contamination.
performance, change the top filter (when possible) before trying alternative cleaning
methods. Care should be taken when changing a filter as this can affect column
packing and interfere with performance.

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 0.6 ml/min (HiScreen 4.7 ml),
3 ml/min (HiPrep 20 ml), or at 40 cm/h with a contact time of 1 to 2 h for Sepharose
High Performance packed in larger columns.
1. Wash with at least 2 CV of 2 M NaCl at 0.6 ml/min (HiScreen 4.7 ml) 1 ml/min
(HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 3 ml/min (HiPrep 20 ml), or at 40 cm/h with a
contact time of 1 to 2 h for Sepharose High Performance packed in larger columns.
5. Wash with at least 4 CV of start buffer or storage buffer until eluent pH and
To remove precipitated proteins, lipids, hydrophobically bound proteins, or lipoproteins,
refer to Appendix 1.
Chemical stability
For daily use, Sepharose High Performance media are stable in all common, aqueous buffers,
1 M NaOH, denaturing agents (8 M urea, 6 M guanidine hydrochloride), 70% ethanol, 1 M acetic
acid, 30% acetonitrile, and with additives such as nonionic detergents.
Sepharose High Performance can be used with organic solvents such as dimethylsulfoxide,
dimethylformamide, tetrahydrofuran, acetone, chloroform, dichloromethane, dichloroethane,
and dichloroethane/pyridine (50:50) as well as polar solvents and aqueous/organic isolutions.
The water in the medium can be exchanged by the alternative solvent with very little effect on
the pore size of the matrix.
Avoid cationic detergents with SP Sepharose High Performance. Avoid anionic
detergents with Q Sepharose High Performance. Avoid oxidizing agents.
Storage
0.2 M sodium acetate in the 20% ethanol solution for columns packed with SP Sepharose
High Performance. Degas the ethanol/water mixture thoroughly and apply at a low flow rate
to avoid overpressuring the column. Store at room temperature or, for long periods, store at
4C to 8C. Ensure that the column is sealed well to avoid drying out. Whenever possible, use
the storage and shipping device if supplied by the manufacturer. Store unused media at 4C to
30C in 20% ethanol. Do not freeze.
To avoid formation of air bubbles in a packed column, ensure that column and buffers
are at the same temperature when preparing for a run.
11000421 AC 81
Sepharose Fast Flow: purification with good resolution and easy scale-up
Use Sepharose Fast Flow for capture or intermediate purification steps that require
good resolution (flow velocity up to 300 cm/h).
Use a weak ion exchanger such as DEAE, CM, or ANX Sepharose Fast Flow, if a strong
ion exchanger (substituted with Q or SP) does not give the required selectivity.
Run Sepharose Fast Flow columns on KTA chromatography systems, HPLC systems, or
systems using peristaltic pumps. Appendix 4 provides guidance on selecting the right
KTA system.
Sepharose Fast Flow media are based on a matrix of 90 m particles made from 6% agarose
and highly cross-linked for chemical and physical stability. ANX Sepharose 4 Fast Flow (high
sub) is based on 4% agarose to form a medium that maintains a high binding capacity when
separating large molecules such as thyroglobulin (Mr = 650 000), particularly suitable for largescale production when total binding capacity becomes economically significant.
Sepharose Fast Flow matrices are substituted with a range of ion exchange groups (Q, DEAE,
ANX, SP, and CM) giving the opportunity to test and use different selectivities (see Chapter 1
for an explanation of strong and weak ion exchangers). Ion exchangers containing strong ion
exchange groups (Q and SP) maintain their charge over a broad pH range, allowing selection of
the most suitable pH for each application.
Ion exchangers containing weak ion exchange groups (DEAE, CM, and ANX) offer alternative
selectivities, but over a narrower pH working range. Figure 3.26 illustrates how the selectivity of
Sepharose Fast Flow media changes according to the anion exchange group.
Particle size and bed volumes remain stable, despite changes in ionic strength or pH, to ensure
fast separations at high flow rates with good resolution. Methods can be easily scaled up from
columns such as HiTrap Q FF (1 ml, prepacked with Q Sepharose Fast Flow) through to largescale columns such as FineLINE. The performance of Sepharose Fast Flow is well documented
and there are many examples of the smooth transfer from the laboratory to pilot scale and on
to production.
II
Columns:
(A)
HiT rap AN X FF
(high sub), 1 ml
300
50
III
I
40
250
II
III
(B)
HiT rap Q XL, 1 ml
A 280 nm
30
II
150
III
(C)
I
HiTrap Q FF, 1 ml
20
200
(A) HiTrap ANX FF (high sub), 1 ml

(B) HiTrap Q XL, 1 ml
(C) HiTrap Q FF, 1 ml
(D) HiTrap DEAE FF, 1 ml
Sample:
0.4 mg conalbumin (pI = 6.3),
0.8 mg a-lactoglobulin (pI = 5.8),
1.2 mg soya bean trypsin inhibitor (pI = 4.5)
dissolved in 2 ml start buffer
Sample volume: 2 ml
Start buffer:
20 mM Tris-HCl pH 7.4
Elution buffer: 20 mM Tris-HCl, 500 mM NaCl pH 7.4
Flow rate:
1 ml/min (150 cm/h)
Gradient:
0% elution buffer (25 CV),
Wash:
Elution:
5 ml start buffer
40 ml, linear gradient,
0% to 80% elution buffer
100
II
III
(D)
10
HiTrap DEAE FF, 1 ml
50
0
0
10
20
30
40
50
Volume (ml)
Fig 3.26. Separation of conalbumin (I), a-lactalbumin (II) and soya bean trypsin inhibitor (III) on a range of anion
exchange HiTrap columns demonstrates the difference in selectivity according to the anion exchange group.
82 11000421 AC
Composition:
Sulfopropyl (SP), carboxymethyl (CM), quaternary amino (Q) or diethylaminoethyl (DEAE)
groups coupled to highly cross-linked 6% agarose via chemically stable ether bonds
Diethylaminopropyl (ANX) group coupled to highly cross-linked 4% agarose via chemically
stable ether bonds
The characteristics of Sepharose Fast Flow media are shown in Table 3.12.
Table 3.12. Characteristics of Sepharose Fast Flow media
Product
Functional group
-CH2-N+-(CH3)3
-CH2-CH2-CH2-SO3-
-CH2-CH2-N+-(CH2-CH3)2
ANX Sepharose 4 Fast Flow
-CH2-CHOH-CH2-N+-(CH2-CH3)2
-CH2-COO -
pH stability1
Long term: 2 to 12
Short term: 2 to 14
Long term: 4 to 13
Short term: 3 to 14
Long term: 2 to 12
Short term: 2 to 14
Long term: 3 to 13
Short term: 2 to 14
Long term: 4 to 13
Short term: 2 to 14
Mean particle
size (m)
90
90
90
90
90
side effects on the chromatography performance. Short-term, pH stability refers to the pH interval for regeneration,
Sepharose Fast Flow media, with a range of selectivities, are available prepacked in HiTrap,
HiScreen, and HiPrep columns and in media packs (Fig 3.27). Purification options for the media
and prepacked columns are shown in Table 3.13.
Fig 3.27. The range of Sepharose Fast Flow is available in media packs and prepacked HiTrap, HiPrep, and
HiScreen columns. The media are also available in high-throughput process development (HTPD) format,
see Chapter 5, Large-scale purification.
11000421 AC 83
Table 3.13. Purification options for Sepharose Fast Flow media and prepacked columns
Product

column or per ml medium
Recommended Maximum Working

working flow1 flow1
pH range2
Maximum
operating
back pressure3
(MPa/psi)
1 MPa = 10 bar

3 mg/ml (thyroglobulin, Mr 669 000) 50 to 400 cm/h 750 cm/h

120 mg/ml (HSA, Mr 68 000)
110 mg/ml, (alactalbumin,
Mr 14 300)
2 to 12
0.3/43
HiTrap Q FF, 1 ml
3 mg (thyroglobulin, Mr 669 000) up to 1 ml/min 4 ml/min

120 mg (HSA, Mr 68 000)
110 mg (alactalbumin, Mr 14 300)
2 to 12
0.3/43
HiTrap Q FF, 5 ml
15 mg (thyroglobulin, Mr 669 000) up to 5 ml/min 20 ml/min 2 to 12

600 mg (HSA, Mr 68 000)
0.3/43
HiScreen Q FF, 4.7 ml
120 mg/ml (HSA, Mr 68 000)
3.5 ml/min 2 to 12
0.15/22
HiPrep Q FF 16/10, 20 ml 60 mg (thyroglobulin, Mr 669 000) 2 to 10 ml/min 10 ml/min 2 to 12

2400 mg (HSA, Mr 68 000)
0.15/22
2.3 ml/min
Weak anion exchangers

2 to 9
0.3/43
50 to 300 cm/h 400 cm/h

43 mg/ml (BSA, Mr 67 000)
5 mg/ml (thyroglobulin, Mr 669 000)
3 to 10
0.1/14
100 mg (alactalbumin, Mr14 300)

110 mg (HSA, Mr 68 000)
2 to 9
0.3/43
500 mg (alactalbumin, Mr 14 300) up to 5 ml/min 20 ml/min 2 to 9

550 mg (HSA, Mr 68 000)
0.3/43
HiScreen DEAE FF
110 mg (HSA, Mr 68 000)
3.5 ml/min 2 to 9
0.15/22
HiPrep DEAE FF 16/10,

20 ml
2000 mg (alactalbumin, Mr 14 300) 2 to 10 ml/min 10 ml/min 2 to 9

2200 mg (HSA, Mr 68 000)
0.15/22
HiTrap ANX FF
(high sub), 1 ml
43 mg (BSA, Mr 67 000)
5 mg (thyroglobulin, Mr 669 000)
3 to 10
0.3/43
HiTrap ANX FF
(high sub), 5 ml
215 mg (BSA, Mr 67 000)
25 mg (thyroglobulin, Mr 669 000)
0.3/43
DEAE Sepharose
Fast Flow
100 mg/ml (alactalbumin,

Mr 14 300)
110 mg/ml (HSA, Mr 68 000)
ANX Sepharose 4 Fast

Flow (high sub)
50 to 400 cm/h 750 cm/h
2.3 ml/min

50 to 400 cm/h 750 cm/h
SP Sepharose Fast Flow 50 mg/ml (bovine COHb,
Mr 69 000)
50 mg/ml (human IgG, Mr 160 000)
70 mg/ml (ribonuclease A, Mr 13 700)
4 to 13
0.3/43
HiTrap SP FF, 1 ml
50 mg (bovine COHb, Mr 69 000) up to 1 ml/min 4 ml/min

50 mg (human IgG, Mr 160 000)
70 mg (ribonuclease A, Mr 13 700)
4 to 13
0.3/43
HiTrap SP FF, 5 ml
250 mg (bovine COHb, Mr 69 000) up to 5 ml/min 20 ml/min 4 to 13

250 mg (human IgG, Mr 160 000)
0.3/43
HiScreen SP FF, 4.7 ml
110 mg/ml (HSA, Mr 68 000)
3.5 ml/min 4 to 13
0.15/22
HiPrep SP FF 16/10, 20 ml 1000 mg (bovine COHb, Mr 69 000) 2 to 10 ml/min 10 ml/min 4 to 13

1000 mg (human IgG, Mr 160 000)
0.15/22
84 11000421 AC
2.3 ml/min
Table 3.13 cont.

working flow1 flow1
pH range2
Maximum
operating
back pressure3
(MPa/psi)
1 MPa = 10 bar
50 to 400 cm/h 750 cm/h
6 to 10
0.3/43
HiTrap CM FF, 1 ml
50 mg (ribonuclease A, Mr 13 700) up to 1 ml/min 4 ml/min
6 to 10
0.3/43
HiTrap CM FF, 5 ml
250 mg (ribonuclease A, Mr 13 700) up to 5 ml/min 20 ml/min 6 to 10
0.3/43

column or per ml medium
Product
Weak cation exchangers
CM Sepharose Fast Flow 50 mg/ml medium

(ribonuclease A, Mr 13 700)
HiPrep CM FF 16/10, 20 ml 1000 mg (ribonuclease A, Mr 13 700) 2 to 10 ml/min 10 ml/min 6 to 10

1
2
3
0.15/22
Use prepacked HiPrep columns (20 ml) for method development, group separations,
larger scale purification, sample concentration or clean-up. Connect several HiPrep
columns in series to increase binding capacity.
Use prepacked HiScreen columns (4.7 ml, bed height 10 cm) for method development
and screening before scaling up with bed height maintained.
For column packing in Tricorn and XK columns, see Table 3.14. Select a production column such
as BPG or Chromaflow for larger volumes.
Table 3.14. Packing volumes and bed heights for Sepharose Fast Flow media packed in Tricorn and XK columns
Column
Volume (ml)
Bed height (cm)
Tricorn 10/100
up to 8
up to 10
Tricorn 10/150
up to 12
up to 15
Tricorn 10/200
up to 16
up to 20
XK 16/20
up to 30
up to 15
XK 26/20
up to 80
up to 15
XK 26/40
up to 196
> 15
XK 50/20
up to 274
up to 14
XK 50/30
up to 559
up to 28.5
Media scouting
Using 1 ml HiTrap columns the most suitable matrix and charged group for a separation can be
quickly and easily selected before optimization and scale-up. In Figure 3.28, a comparison of
elution profiles for the same sample separated under identical conditions on three different
Sepharose media illustrates the differences in selectivity and resolution that can result from
changing the charge group and the particle size. The most suitable medium can be selected
and conditions optimized according to the requirements for the separation, for example to
isolate a single, well-resolved peak or to maximize resolution between several peaks of interest.
11000421 AC 85
Begin by scouting on the strong ion exchangers (Q, S, or SP) in order to find the greatest
differences in charge between the molecules of interest.
Columns:
(A) HiTrap SP XL, 1 ml

(B) HiTrap SP FF, 1 ml
(C) HiTrap CM FF, 1 ml
Sample:
3 mg ribonuclease A (pI = 9.3),
0.8 mg cytochrome C (pI = 10.3),
0.8 mg lysozyme (pI > 11.0)
Sample volume:
2 ml in start buffer
Start buffer:
Elution buffer:
20 mM sodium phosphate, 500 mM NaCl pH 6.8
Flow rate (flow velocity): 1 ml/min (150 cm/h)
Gradient:
I
III
(A)
HiT rap SP XL, 1 ml
40.0
II
150
A 280 nm
100
II+III
20.0
I
(C)
50
HiT rap CM FF, 1 ml

,
II
30.0
(B)
HiT rap SP FF, 1 ml
III
10.0
0
0
20
40
Volume (ml)
60
Fig 3.28. Media scouting: separation of ribonuclease A (I), cytochrome C (II), and lysozyme (III) on
HiTrap CM FF 1 ml, HiTrap SP FF 1 ml, and HiTrap SP XL 1 ml.
Capture
An example of capture using Sepharose DEAE Fast Flow medium prepacked in
HiPrep DEAE FF 16/10 is shown in Figure 3.29.
2.0
4.0
Column:
Sample:
The phosphatase activity is

represented by the green bars.
2.0
A 405 nm
A 280 nm
3.0
Start buffer:
EDTA,
HiPrep DEAE FF 16/10, 20 ml

200 ml clarified E. coli supernatant,
diluted 1:2 with water, pH 6.6,
conductivity 2.6 mS/cm
25 mM Tris-HCl, 10% glycerol, 1 mM
2 mM DTT, pH 7.4
1 M NaCl, 25 mM Tris-HCl, 10% glycerol,
1 mM EDTA, 2 mM DTT, pH 7.4
Gradient:
Elution buffer:
1.0
0
300
500
Volume (ml)
700
900
Fig 3.29. A HiPrep DEAE FF 16/10 column is used as the capture step to concentrate rPhosphatase and
remove most of the contaminants.
Scaling-up
Figure 3.30 shows the ease with which separations can be scaled up on columns prepacked
with Sepharose Fast Flow. Beginning with a 1 ml HiTrap column the reproducibility of the
separation has been maintained through a 20-fold scale-up.
86 11000421 AC
(A)
Sample:
1. Conalbumin, 2 mg/ml
2. a-lactalbumin, 4 mg/ml
3. Soy trypsin inhibitor, 6 mg/ml
Sample volume:
1 CV
(A) 1 ml, (B) 5 ml, (C) 20 ml
Start buffer:
Elution buffer:
50 mM Tris-HCl, 500 mM NaCl, pH 7.3
Flow velocity (flow rates): 150 cm/h (1 ml/min using HiTrap 1 ml,
5 ml/min using HiTrap 5 ml and
HiPrep 16/10 columns)
Gradient:
(B) 20 ml, (B) 100 ml, (C) 400 ml
HiTrap Q FF, 1 ml
15
A 280 nm
3
10
1
5
0
0
10
15
20
25
30
Volume (ml)
(B)
(C)
2
HiTrap Q FF, 5 ml
25
20
20
A 280 nm
A 280 nm
HiPrep Q FF 16/10, 20 ml
25
15
1
10
15
1
10
5
50
0
0
20
40
60
80
100
Volume (ml)
120
140
100
200
300
400
500
Volume (ml)
Fig 3.30. Five-fold and 20-fold scale-up using prepacked Q Sepharose Fast Flow prepacked columns.
It can be an advantage to concentrate a sample prior to SEC in order to minimize sample
volume and facilitate a rapid, high-resolution size separation. HiTrap columns offer a
convenient, ready-to-use solution for sample concentration. Table 3.11 earlier in the chapter
gives examples of the high concentration factors achieved when concentrating proteins
from very dilute starting material using HiTrap columns prepacked with Sepharose High
Performance medium. Similar results can be achieved with HiTrap columns prepacked with
Filter buffers after all salts and additives have been included. Use high quality water and
chemicals. Filter solutions using filters of 1 m or less. To avoid formation of air bubbles
in a packed column, maintain buffers and columns at a constant temperature before
and during a run.
substance when using an anion exchanger (Q, DEAE, or ANX) and 0.5 to 1.0 pH unit
below the pI of the target substance when using a cation exchanger (SP, CM). See
Appendix 2 for recommendations on volatile and nonvolatile buffer systems for anion
and cation exchangers.
11000421 AC 87

anion exchange (Q)
cation exchange (SP)
If selectivity is not satisfactory when using a strong ion exchanger (Q or SP), try a weak
ion exchanger (DEAE, ANX, or CM) instead.

1. To remove ethanol, wash with 1 CV of distilled water at 1 ml/min (HiTrap 1 ml, HiScreen
4.7 ml), 5 ml/min (HiTrap 5 ml), 2 ml/min (HiPrep 20 ml), or at 50 cm/h for Sepharose Fast
Flow packed in larger columns. This step ensures removal of ethanol and avoids the
risk of precipitation if buffer salts were to come into contact with the ethanol. The step
can be omitted if precipitation is not likely to be a problem.
2. Wash with 5 CV of start buffer at 1 ml/min (HiTrap 1 ml), 2.3 ml/min (HiScreen 4.7 ml),
5 ml/min (HiTrap 5 ml), or 5 ml/min (HiPrep 20 ml).

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 2.3 ml/min (HiScreen 4.7 ml),
5 ml/min (HiPrep 20 ml), or at 150 cm/h for Sepharose Fast Flow packed in larger columns.
2. Adjust the sample to the chosen starting pH and ionic strength and apply to the
column.
are stable i.e. when all unbound material has washed through the column.
88 11000421 AC

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 2.3 ml/min (HiScreen 4.7 ml), 5 ml/min
(HiPrep 20 ml), or at 150 cm/h for Sepharose Fast Flow packed in larger columns.
been eluted.
7. Re-equilibrate 5 to 10 CV of start buffer or until eluent pH and conductivity reach the
required values.
Refer to Chapter 2 for advice on optimizing the separation.
Check column performance regularly by determining column efficiency and peak symmetry,
see Appendix 3. Note that Appendix 3 does not apply to HiTrap or HiPrep columns.
Cleaning
performance, a slow flow rate, increasing back pressure or complete blockage are all
methods. Care should be taken when changing a filter as this can affect the column
11000421 AC 89

Flow rates: 1 ml/min (HiTrap 1 ml, HiScreen 4.7 ml), 5 ml/min (HiTrap 5 ml), 5 ml/min
(HiPrep 20 ml), or at 40 cm/h with a contact time of 1 to 2 h for Sepharose Fast Flow
packed in larger columns.
4. Rinse with at least 2 CV of distilled water (same flow as step 1) until the UV-baseline
and the eluent pH are stable.
5. Wash with at least 4 CV of start buffer or storage buffer until eluent pH and conductivity
have reached the required values.
To remove precipitated proteins, lipids, hydrophobically bound proteins, or lipoproteins, refer
to Appendix 1.
Chemical stability
For daily use, Sepharose Fast Flow media are stable in all common, aqueous buffers, 1 M NaOH,
denaturing agents (8 M urea, 6 M guanidine hydrochloride), with additives such as nonionic
detergents, 70% ethanol, 1 M acetic acid, and 30% isopropanol.
Sepharose Fast Flow can be used with organic solvents such as dimethylsulfoxide,
dimethylformamide, tetrahydrofuran, acetone, chloroform, dichloromethane, dichloroethane, and
dichloroethane/pyridine (50:50) as well as polar solvents and aqueous/organic isolutions. The
water in the medium can be exchanged by the alternative solvent with very little effect on the
pore size of the matrix.
Avoid cationic detergents with SP or CM Sepharose Fast Flow. Avoid anionic detergents
with Q, DEAE, or ANX Sepharose Fast Flow. Avoid oxidizing agents.
Storage
0.2 M sodium acetate in the 20% ethanol solution for SP Sepharose Fast Flow. Degas the ethanol/
water mixture thoroughly and apply at a low flow rate to avoid over-pressuring the column.
Store at room temperature or, for long periods, store at 4C to 8C. Ensure that the column
is sealed well to avoid drying out. Whenever possible, use the storage and shipping device if
supplied by the manufacturer. Store unused media at 4C to 30C in 20% ethanol. Do not freeze.
90 11000421 AC
Sepharose XL: for selected proteins that require very high binding
capacity to increase productivity, easy scale-up
Use Sepharose XL media for purification of proteins when improved binding capacity
compared to other Sepharose media has been confirmed for the selected protein.
Use Sepharose XL at the beginning of a purification scheme for initial capture when
a high binding capacity and rapid separation is required for a selected protein from
clarified samples.
Run columns packed with Sepharose XL on systems such as KTA, HPLC, or systems
using peristaltic pumps. Appendix 4 provides guidance on selecting the right KTA system.
Sepharose XL media are based on a matrix of 90 m particles, made from 6% agarose and
highly cross-linked for chemical and physical stability, substituted with quaternary ammonium
(Q) or sulfopropyl (SP) groups. The ionic groups are bound to long, flexible dextran chains which
have been coupled to the agarose. This increases the exposure of the Q or SP groups thereby
raising the binding capacity to a very high level without restricting the passage of charged
molecules. The strong ion exchange groups maintain their charge over a broad pH range,
allowing selection of the most suitable pH for each application. Particle size and bed volumes
remain stable, despite changes in ionic strength or pH, to ensure fast separations at high flow
rates with good resolution.
Composition: sulfopropyl (SP) or quaternary amino (Q) groups attached via chemically stable
ether bonds to long, flexible dextran chains that are covalently coupled to highly cross-linked
6% agarose (Table 3.15).
Table 3.15. Characteristics of Sepharose XL media
Product
Functional group
pH stability1
Q Sepharose XL
-CH2-N -(CH3)3
Long term: 2 to 12
Short term: 2 to 14
90
SP Sepharose XL
-CH2-CH2-CH2-SO3-
Long term: 4 to 13
Short term: 3 to 14
90
Q and SP Sepharose XL are available in chromatography media packs as well as convenient
prepacked HiTrap columns for small-scale purification and HiPrep columns for scale-up
(Fig 3.31). Purification options for the media and prepacked columns are shown in Table 3.16.
Fig 3.31. Q and SP Sepharose XL are available in prepacked HiTrap and HiPrep columns, in
chromatography media packs, and in the HiTrap IEX Selection Kit, 17600233.
11000421 AC 91
Table 3.16. Purification options for Sepharose XL media and prepacked columns
Binding capacity
per column or per
ml medium
Product

working flow1 flow1
pH range2
Maximum
operating
back pressure3
(MPa/psi)
1 MPa = 10 bar

Q Sepharose XL
> 130 mg/ml (BSA,

Mr 67 000)
300 to
500 cm/h
HiTrap Q XL, 1 ml
> 130 mg (BSA,

Mr 67 000)
2 to 12
0.3/43
HiTrap Q XL, 5 ml
> 650 mg (BSA,

Mr 67 000)
0.3/43
2 to 10 ml/min 10 ml/min 2 to 12
0.15/22
HiPrep Q XL 16/10, 20 ml > 2600 mg (BSA,

Mr 67 000)
700 cm/h 2 to 12
0.3/43

SP Sepharose XL
> 160 mg/ml (lysozyme, 300 to

Mr 14 500)
500 cm/h
HiTrap SP XL, 1 ml
> 160 mg (lysozyme,

Mr 14 500)
4 to 13
0.3/43
HiTrap SP XL, 5 ml
> 800 mg (lysozyme,

Mr 14 500)
0.3/43
2 to 10 ml/min 10 ml/min 4 to 13
0.15/22
HiPrep SP XL 16/10, 20 ml > 3200 mg (lysozyme,

Mr 14 500)
1
2
3
700 cm/h 4 to 13
0.3/43
See Appendix 5 to convert linear flow (cm/h) to volumetric flow rate (ml/min) and vice versa.
Use prepacked HiPrep columns (20 ml) for method development, group separations,
larger scale purification, sample concentration or clean-up. Connect several HiPrep
columns in series to increase binding capacity.
For column packing in Tricorn and XK columns, see Table 3.17. Select a production column such
as BPG or Chromaflow for larger volumes.
Table 3.17. Packing volumes and bed heights for Sepharose XL media packed in Tricorn and XK columns
Column
Volume (ml)
Bed height (cm)
Tricorn 10/100
up to 8
up to 10
Tricorn 10/150
up to 12
up to 15
Tricorn 10/200
up to 16
up to 20
XK 16/20
up to 30
up to 15
XK 26/20
up to 80
up to 15
XK 26/40
up to 196
> 15
XK 50/20
up to 274
up to 14
XK 50/30
up to 559
up to 28.5
92 11000421 AC
Media selection
The most suitable matrix and charged group for a separation can be selected quickly and easily
by using 1 ml HiTrap columns. In Figure 3.32, a comparison of elution profiles for the same sample
separated under identical conditions on three different media illustrates the differences in
selectivity and resolution that can result from changing the charge group and matrix. The most
suitable medium can be selected and conditions optimized according to the requirements for
the purification. In this example, Sepharose XL resolves the three components and optimization
of elution conditions could further improve the resolution. However, any of these media would
be suitable if the aim was to isolate the first major peak (ribonuclease A).
I
Columns:
(A)
III
HiTrap SP XL, 1 ml
40
II
(B)
30
HiT rap SP FF, 1 ml
100
II+III
20
(C)
50
II
HiTrap CM FF, 1 ml
A 280 nm
150
(A) HiTrap SP XL, 1 ml

(B) HiTrap SP FF, 1 ml
(C) HiTrap CM FF, 1 ml
Sample:
3 mg ribonuclease A (pI = 9.3),
0.8 mg cytochrome C (pI = 10.3),
0.8 mg lysozyme (pI > 11)
Sample volume:
2 ml in start buffer
Start buffer:
Elution buffer:
20 mM sodium phosphate,
500 mM NaCl pH 6.8
Gradient:
0% elution buffer (25 CV), 0% to
III
10
0
0
20
40
Volume (ml)
60
Fig 3.32. Media scouting: separation of ribonuclease A (I), cytochrome C (II), and lysozyme (III) on a range of
anion exchange HiTrap columns.
Capture
Capture of alkaline phosphatase from a clarified lysate of E. coli using a HiTrap Q XL 1 ml column
is shown in Figure 3.33. Separation was monitored at A280 nm and phosphatase activity
assayed by a spectrophotometric method at A405 nm.
50
A 405 nm
600
A 280 nm
30
400
300
20
200
10
100
0
0
10
20
40
30
Volume (ml)
50
60
40
500
Columns:
Sample:
Sample volume:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
HiTrap Q XL, 1 ml
2 ml of E.coli lysate clarified by centrifugation
2 ml
20 mM Tris-HCl, 500 mM NaCl, pH 7.4
1 ml/min (150 cm/h)
Fig 3.33. Clarified E. coli lysate on HiTrap Q XL, absorbance values at 450 nm relate to phosphatase activity
in eluted fractions.
11000421 AC 93
Capture and scale-up

Figure 3.34 shows a pilot scale purification performed on a Sepharose XL ion exchanger.
The separation was developed on Q Sepharose XL packed in an XK 16/20 column in order to
select optimal pH and to determine maximum binding capacity available. Adding CaCl2 to
the sample precipitated DNA and so increased the binding capacity for the target protein. Final
loading was reduced to 75% of the maximum capacity and the result verified before scaling-up
to a larger, INdex column.
Column:
Sample:
Q Sepharose XL in INdEX 70 column, 385 ml bed volume

Recombinant a-amylase produced in E. coli, homogenized,
2.2 l diluted in distilled water to 15.4 l, 7.2 mS/cm, 10 mM CaCl2, centrifuged
Start buffer: 20 mM Tris-HCl, pH 8.0, 10 mM CaCl2
Elution buffer: 20 mM Tris-HCl, pH 8.0, 1 M NaCl, 10 mM CaCl2
Flow flow:
300 cm/h, 12 l/h
Gradient:
20 CV 0 to 1 M NaCl
Eluent:
1.48 l, 3.8 CV
Spec. act. a-amylase 6420 U/l
A 280 nm
500
Volume (ml)
1000
Fig 3.34. Capture of recombinant a-amylase from E. coli on Q Sepharose XL pilot scale column. The first
peak during gradient elution contained -amylase.
It can be an advantage to concentrate a sample prior to SEC in order to minimize sample
volume and facilitate a rapid, high resolution size separation. HiTrap columns offer a
convenient, ready-to-use solution for sample concentration. Table 3.9 earlier in the chapter
gives examples of the high concentration factors achieved when concentrating proteins
from very dilute starting material using HiTrap columns prepacked with Sepharose High
Performance medium. Similar results can be achieved with HiTrap columns prepacked with
Guidelines for selection of media, buffer, pH and ionic strength conditions, and method
and chemicals. Filter solutions using filters of 1 m or smaller. To avoid formation of air
bubbles in a packed column, maintain buffers and columns at a constant temperature
before and during a run.
94 11000421 AC
The pH of the start buffer should be at least 0.5 to 1.0 pH unit above the pI of the
target substance when using an anion exchanger (Q) and 0.5 to 1.0 pH unit below the
pI of the target substance when using a cation exchanger (SP). See Appendix 2 for
recommendations on volatile and nonvolatile buffer systems for anion and
cation exchangers.
anion exchange (Q)
cation exchange (SP)

1. To remove ethanol, wash with 1 CV of distilled water at 1 ml/min (HiTrap 1 ml), 5 ml/min
(HiTrap 5 ml), 5 ml/min (HiPrep 20 ml), or at 50 cm/h for Sepharose XL packed in larger
columns. This step ensures removal of ethanol and avoids the risk of precipitation if
buffer salts were to come into contact with the ethanol. The step can be omitted if
precipitation is not likely to be a problem.
2. Wash with 5 CV of start buffer at 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 5 ml/min
(HiPrep 20 ml), or at 150 cm/h for Sepharose XL packed in larger columns.
5. Run a blank elution before applying sample.

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 5 ml/min (HiPrep 20 ml), or at
150 cm/h for Sepharose XL packed in larger columns. Collect fractions throughout the
separation.
1. Equilibrate column with 5 to 10 CV of start buffer or until the baseline, eluent pH and
6. Re-equilibrate 5 to 10 CV of start buffer or until eluent pH and conductivity reach the
required values.
11000421 AC 95

150 cm/h for Sepharose XL packed in larger columns.
been eluted.
UV baseline, eluent pH and/or conductivity are stable.
Organic solvents such as ethanol can be used to remove nonionic detergents. When selecting
an organic solvent, check the chemical stability of the medium to determine a suitable
concentration.
Cleaning
performance, a slow flow rate, increasing back pressure, or complete blockage are all
96 11000421 AC

40 cm/h with a contact time of 1 to 2 h for Sepharose XL packed in larger columns.
2. Wash with at least 4 CV of 1 M NaOH (same flow as step 1).
3. Wash with at least 2 CV of 2 M NaCl (same flow as step 1).
5. Wash with at least 4 CV of start buffer or storage buffer (same flow as step 1) until
eluent pH and conductivity have reached the required values.
Appendix 1.
Chemical stability
For daily use, Sepharose XL media are stable in all common, aqueous buffers, 1 M NaOH,
detergents, 70% ethanol, 1 M acetic acid, and 30% isopropanol.
Sepharose XL can be used with organic solvents such as dimethylsulfoxide, dimethyl-formamide,
tetrahydrofuran, acetone, chloroform, dichloromethane, dichloroethane, and dichloroethane/
pyridine (50:50) as well as polar solvents and aqueous/organic isolutions. The water in the medium
can be exchanged by the alternative solvent with very little effect on the pore size of the matrix.
Avoid cationic detergents with SP Sepharose XL. Avoid anionic detergents with
Q Sepharose XL. Avoid oxidizing agents.
Storage
0.2 M sodium acetate in the storage solution for SP Sepharose XL. Degas the ethanol/water
mixture thoroughly and apply at a low flow rate to avoid overpressuring the column. Store at
room temperature or, for long periods, store at 4C to 8C. Ensure that the column is sealed well
to avoid drying out. Whenever possible, use the storage and shipping device if supplied by the
manufacturer. Store unused media at 4C to 30C in 20% ethanol. Do not freeze.
11000421 AC 97
Sepharose Big Beads: purification from crude, viscous samples

at large scale
Use Sepharose Big Beads for purification of proteins from crude, viscous samples.
Use Sepharose Big Beads when handling large volumes of crude or viscous samples
that must be bound rapidly and when resolution is less important.
Use Sepharose Big Beads for capture steps, when viscosity and back pressure can limit
the throughput attainable with ion exchangers of smaller particle size.
Run columns packed with Sepharose Big Beads on systems such as KTA, HPLC, or
systems using peristaltic pumps. Appendix 4 gives guidance on how to select the most
suitable KTA system.
Sepharose Big Beads are ion exchangers designed for large-scale industrial applications.
Sepharose Big Beads are based on 100 to 300 m, cross-linked 6% agarose particles,
substituted with quaternary ammonium (Q) or sulfopropyl (SP) groups. The large particle
size, together with a high degree of cross-linking for extreme physical and chemical stability,
ensures that high flow rates can be maintained when processing very viscous samples. For
example, a flow of 500 cm/h can be maintained in an industrial process at viscosities up to
2.5 times the viscosity of water. More dilute samples can be run at 1000 cm/h. Particle size and
bed volumes remain stable, despite changes in ionic strength or pH. The strong ion exchange
groups (Q and SP) maintain their charge over a broad pH range, allowing selection of the most
suitable pH for each application.
Figures 3.35 and 3.36 show the excellent flow characteristics and typical binding capacities for
Sepharose Big Beads media.
BPG 300/20 cm/dist.water/25C
3000
PP113/30 cm/65% ethanol/20C,

viscosity 2.5 times water
2000
1000
2
Pressure (bar)
C/Co, % (concentration in eluate, C as fraction of concentration in sample, Co)

concentration in eluate (C) as fraction of
concentration in sample (Co)
Fig 3.35. Sepharose Big Beads allow high flow rates with high-viscosity samples.
BSA (300 cm/h)
-lactogl. (300 cm/h)
BSA (12 cm/h)
-lactogl. (12 cm/h)
80
C/Co, (%)1
60
40
20
100
200
Binding capacity (mg protein/ml medium)

1
Concentration in eluate (C) as fraction of concentration in sample (Co).
Fig 3.36. Typical binding capacities of SP Sepharose Big Beads. Binding capacity measured in acetate pH 5.0
for bovine serum albumin (BSA) and formate pH 4.1 for b-lactoglobulin at flow velocities of 12 and 300 cm/h.
98 11000421 AC
Composition: sulfopropyl (SP) or quaternary amino (Q) groups coupled to highly cross-linked 6%
agarose via chemically stable ether bonds, see Table 3.18.
Table 3.18. Characteristics of Sepharose Big Beads
Product
Functional group
pH stability1
-CH2-N+-(CH3)3
Long term: 2 to 12
Short term: 2 to 14
200
-CH2-CH2-CH2-SO3-
Long term: 4 to 13
Short term: 3 to 14
200

Q Sepharose Big Beads
SP Sepharose Big Beads
1
Purification options for Q and SP Sepharose Big Beads are described in Table 3.19.
Table 3.19. Purification options for Sepharose Big Beads
Product
Binding capacity
per column or per
ml medium
Recommended Maximum
working flow1
flow1
Working
pH range2
Maximum
operating
back pressure3
(MPa/psi)
1 MPa = 10 bar

Q Sepharose Big Beads Tested for each
up to 300 cm/h
specific application
1800 cm/h 2 to 12
0.3/43
1800 cm/h 4 to 13
0.3/43

SP Sepharose Big Beads Tested for each
up to 300 cm/h
specific application
1
2
3
For column packing in XK columns during method development, particularly when handling
crude, viscous samples, see Table 3.20.
Table 3.20. Packing volumes and bed heights for Sepharose Q and SP High Performance packed in XK columns
Column
Volume (ml)
Bed height (cm)
XK 16/20
up to 30
up to 15
XK 26/20
up to 80
up to 15
XK 26/40
up to 196
> 15
XK 50/20
up to 274
up to 14
XK 50/30
up to 559
up to 28.5
Select a production scale column such as BPG or Chromaflow for larger volumes. Sepharose
11000421 AC 99
Big Beads can be packed in large scale columns by applying constant pressure between
0.1 to 0.3 MPa (1.0 to 3.0 bar, 14.5 to 43.5 psi) by slurry sedimentation followed by adapter
compression, or by suction packing. Follow the instructions supplied with the medium.
Guidelines for selection of media, buffer, pH, and ionic strength conditions, and method
optimization are given in Chapter 2. See Appendix 2 for recommendations on volatile and
nonvolatile buffer systems.
Correct sample and buffer preparation is essential in order to achieve optimal
separation and avoid any deterioration in column performance. Refer to Chapter 2 and
Appendix 1 for recommendations and advice.
Filter buffers after all salts and additives have been included. Use high quality water and
chemicals. Filter solutions through 1 m filters. To avoid formation of air bubbles in a packed
column, maintain buffers and columns at a constant temperature before and during a run.

1. Wash with 5 CV of distilled water at 300 cm/h.
Gradient or step elution

Conditions for a large scale-purification using Sepharose Big Beads will be determined
during method development and relate to the specific application. Refer to Chapter 2 for
advice on optimizing a separation. Typical separation flow rates should be 200 to 500 cm/h.
Cleaning
Correct preparation of samples and buffers and regeneration with a high salt wash (1 M NaCl)
at the end of each separation should keep most columns in good condition. However, reduced
indications that the medium needs to be cleaned using more stringent procedures in order
to remove contaminants.
100 11000421 AC

1. Wash with at least 2 CV of 2 M NaCl at 40 cm/h for a contact time of 1 to 2 h.
2. Wash with at least 4 CV of 1 M NaOH (same flow as step 1).
3. Wash with at least 2 CV of 2 M NaCl (same flow as step 1).
5. Wash with at least 4 CV of start buffer or storage buffer (same flow as step 1) until
eluent pH and conductivity have reached the required values.
To remove precipitated proteins, lipids, hydrophobically bound proteins, or lipoproteins, refer
to Appendix 1.
Chemical stability
For daily use, Sepharose Big Beads are stable in all common, aqueous buffers, 1 M NaOH,
detergents, 70% ethanol, 1 M acetic acid, 30% acetonitrile, and 30% isopropanol.
Sepharose Big Beads can be used with organic solvents such as dimethylsulfoxide, dimethylformamide, tetrahydrofuran, acetone, chloroform, dichloromethane, dichloroethane and
dichloroethane/pyridine (50:50), as well as polar solvents and aqueous/organic isolutions.
The water in the medium can be exchanged by the alternative solvent with very little effect
on the pore size of the matrix.
Avoid cationic detergents with SP Sepharose Big Beads. Avoid anionic detergents with
Q Sepharose Big Beads. Avoid oxidizing agents.
Storage
200 mM sodium acetate in the storage solution for SP Sepharose Big Beads. For small-scale
columns, degas the ethanol/water mixture thoroughly, for large-scale columns ensure that an
air trap is included before the column. Add storage solution at a low flow rate, checking the back
pressure as the column equilibrates. Alternatively, store at neutral pH in buffer containing 20%
ethanol or in 100 mM NaOH.
Store at room temperature or, for long periods, store at 4C to 8C. Ensure that the column is
sealed well to avoid drying out. Store unused media at 4C to 30C in 20% ethanol. Do not freeze.
11000421 AC 101
Capto: high-flow media with high resolution

Use Capto media, including Capto, Capto ImpRes and Capto ImpAct, for screening of
selectivity and method conditions before scaling up, as well as for small-scale purification.
Use Capto media with high flow-properties for capture, intermediate purification, and
polishing of a wide range of biomolecules.
Run Capto media in an optimal way with liquid chromatography systems such as KTA .
Appendix 4 provides guidance on selecting the right KTA system.
Capto media are based on the high-flow agarose base matrix, which gives excellent
pressure-flow properties, making the media suitable for process- scale applications (Fig 3.37).
500
Capto SP ImpRes
SP Sepharose High Performance
400
300
200
100
0
0
2
3
Pressure (bar)
Fig 3.37. The pressure-flow properties of Capto ImpRes are improved compared with Sepharose High
Performance due to the increased mechanical stability of the base matrix. Running conditions:
Axichrom 300 column, 20 cm bed height with water at 20C.
Capto media are high capacity ion exchangers where the ligands are coupled to a chemically
modified, high-flow agarose matrix. The high-flow agarose matrix provides particle rigidity
without compromising the pore size. This allows for fast mass transfer resulting in high dynamic
binding capacities at high flow rates, making the media suitable for process-scale applications.
Capto Q, Capto S, and Capto DEAE are used for capture and intermediate purification of
proteins. Capto Q ImpRes and Capto SP ImpRes are high-resolution media designed for
intermediate purification and polishing. Capto S ImpAct is especially suitable for intermediate
purification and polishing of MAbs, where a common main challenge is to selectively remove
impurities similar to the target product.
Composition: Quaternary amine (Q), sulfopropyl (SP), and sulfonate (S) coupled to highly cross-linked
high-flow agarose. The characteristics of Capto media are shown in Table 3.21.
102 11000421 AC
Table 3.21. Characteristics Capto media

Product
Functional group
pH stability1
Capto Q
-CH2-N+-(CH3)3
Long term: 2 to 12
Short term: 2 to 14
90
Capto DEAE
-CH2-CH2-N+-(CH2CH3)2
Long term: 2 to 12
Short term: 2 to 14
90
Capto S
-CH2-SO3-
Long term: 4 to 12
Short term: 3 to 14
90
Capto Q ImpRes
-CH2-N+-(CH3)3
Long term: 2 to 12
Short term: 2 to 14
40
Capto SP ImpRes
-CH2-CH2-CH2-SO3-
Long term: 4 to 12
Short term: 3 to 14
40
Capto S ImpAct
-CH2-SO3-
Long term: 4 to 12
Short term: 3 to 14
50
Anion and cation exchanger Capto media are available prepacked in HiTrap and HiScreen columns
and in chromatography media packs (Fig 3.38). Table 3.22 is a presentation of different
Capto media for ion exchange chromatography. Some of the media are also available in
PreDictor filter plates, PreDictor RoboColumn, and ReadyToProcess columns (see Chapter 5,
Large-scale purification).
Fig. 3.38. Capto media are available in bulk packs, and prepacked HiTrap and HiScreen columns,
The media are also available in high-throughput process development (HTPD) format.
11000421 AC 103
Table 3.22. Purification options for Capto media
Binding capacity
Recommended
working
flow rate
Maximum
flow rate
Working
pH range
Capto Q
> 100 mg (BSA)/ml medium
up to 700 cm/h1
700 cm/h1
2 to 12
Capto Q ImpRes
> 55 mg (BSA)/ml medium
up to 220 cm/h1
220 cm/h1
2 to 12
2 to 12
HiTrap Capto Q, 1 ml
> 100 mg (BSA)
1.0 ml/min
4.0 ml/min
HiTrap Capto Q, 5 ml
> 500 mg (BSA)
5.0 ml/min
20.0 ml/min 2 to 12
HiTrap Capto Q ImpRes, 1 ml
> 55 mg (BSA)
1.0 ml/min
4.0 ml/min
2 to 12
HiTrap Capto Q ImpRes, 5 ml
> 275 mg (BSA)
5.0 ml/min
20.0 ml/min 2 to 12
HiScreen Capto Q, 4.7 ml
> 470 mg (BSA)
1.2 ml/min
2.3 ml/min
2 to 12
HiScreen Capto Q ImpRes, 4.7 ml
> 260 mg (BSA)
1.2 ml/min
2.3 ml/min
2 to 12
Weak anion exchangers

Capto DEAE
> 90 mg (ovalbumin)/ml medium up to 700 cm/h1
700 cm/h1
2 to 12
HiTrap Capto DEAE, 1 ml
> 90 mg (ovalbumin)
1.0 ml/min
4.0 ml/min
2 to 12
HiTrap Capto DEAE, 5 ml
> 450 mg (ovalbumin)
5.0 ml/min
20.0 ml/min 2 to 12
HiScreen Capto DEAE, 4.7 ml
> 420 mg (ovalbumin)
1.2 ml/min
2.3 ml/min
2 to 12

Capto S
> 120 mg (lysozyme)/ml medium up to 700 cm/h1
700 cm/h1
4 to 12
Capto SP ImpRes
> 70 mg (lysozyme)/ml medium
up to 220 cm/h1
220 cm/h1
4 to 12
Capto S ImpAct
> 90 mg (lysozyme)/ml medium
HiTrap Capto S, 1 ml
> 120 mg (lysozyme)
up to 220 cm/h
220 cm/h
4 to 12
1.0 ml/min
4.0 ml/min
4 to 12
HiTrap Capto S, 5 ml
> 600 mg (lysozyme)
5.0 ml/min
20.0 ml/min 4 to 12
HiTrap Capto SP ImpRes, 1 ml
> 70 mg (lysozyme)
1.0 ml/min
4.0 ml/min
HiTrap Capto SP ImpRes, 5 ml
> 350 mg (lysozyme)
5.0 ml/min
20.0 ml/min 4 to 12
4 to 12
HiTrap Capto S ImpAct, 1 ml
> 90 mg (lysozyme)
1.0 ml/min
4.0 ml/min
HiTrap Capto S ImpAct, 5 ml
> 450 mg (lysozyme)
5.0 ml/min
20.0 ml/min 4 to 12
4 to 12
HiScreen Capto S, 4.7 ml
> 560 mg (lysozyme)
1.2 ml/min
2.3 ml/min
4 to 12
HiScreen Capto SP ImpRes, 4.7 ml > 330 mg (lysozyme)
1.2 ml/min
2.3 ml/min
4 to 12
HiScreen Capto S ImpAct, 4.7 ml
1.2 ml/min
2.3 ml/min
4 to 12
> 420 mg (lysozyme)
Flow velocity in a 1 m column with 20 cm bed height at 20C using process buffers with the same viscosity as water at
< 0.3 MPa (3 bar, 43.5 psi). See Appendix 5 to convert flow velocities (cm/h) to volumetric flow rate (ml/min) and vice versa.
Molecular weights (Mr) of proteins in the table: BSA, 67 000; ovalbumin, 45 000; lysozyme, 14 500.
Use prepacked HiTrap columns (1 ml or 5 ml) for media selection, group separations,
and small-scale purification.
Use prepacked HiScreen columns (4.7 ml, 10 cm bed height) for method development
and optimization before scaling up.
For column packing: Capto media can be used with most modern chromatography
equipment from laboratory to production scale. Due to the higher rigidity of Capto
media, packing procedures differ slightly compared with Sepharose (for details of
packing laboratory-scale columns, see the appropriate Instructions).
104 11000421 AC
Table 3.23 lists suitable empty columns for packing of Capto media from GE.
Table 3.23. Example of columns suitable for packing of Capto media
Column family
Inner diameter (mm)
Laboratory scale
Tricorn
5, 10
HiScale
16, 26, 50
Pilot and production scale

AxiChrom
50 to 10001
BPG
100 to 3002
1
2
Maximum bed height for AxiChrom 1000 is 20 cm.

Note that the pressure rating of BPG 450 column is too low for Capto ImpRes media.
Capture and scale-up
Capto media belong to the BioProcess range of media that are developed and supported for
production-scale chromatography. The small prepacked column formats, HiTrap 1 ml and 5 ml
and HiScreen (4.7 ml), are convenient to use together with a chromatography system when
developing efficient and robust separation methods. Further development and optimization
using Tricorn or HiScale columns then permits straightforward scale-up. Figure 3.39 shows an
example of scaling up an optimized purification of a-chymotrypsin on Capto S, starting from a
Tricorn column.
11000421 AC 105
Column:
Medium:
Sample:
Column:
Medium:
Sample:
Tricorn 5/100 (bed height 9.7 cm, CV = 1.9 ml)

Capto S
a-chymotrypsin in E. coli homogenate,
4 mg/ml to 50 ml
50 mM sodium acetate, 1 M NaCl, pH 4.8
285 cm/h
0% to 100% 0 CV, 100% 5 CV
2 min
Start buffer:
Elution buffer:
Flow velocity:
Gradient:
Residence time:
XK 16/40 (bed height 20.7 cm, CV = 41.5 ml)

Capto S
4 mg/ml to 1040 ml
624 cm/h
0% to 100% 0 CV, 100% 5 CV
2 min
Start buffer:
Elution buffer:
Flow velocity:
Gradient:
Residence time:
(A)
(B)
3500
4000
Column:
Medium:
Sample:
Start buffer:
Elution buffer:
Flow velocity:
Gradient:
Residence time:
20
40
60
Time (min)
80
Re-equilibration
CIP
0
0
1000
Elution
50
2000
Inlet
Re-equilibration
CIP
Elution
Wash
Inlet
500
A280
A280
1000
100
0
0
100
50
20
40
60
Time (min)
80
100
AxiChrom 50 (bed height 22 cm, CV = 431 ml)

Capto S
4 mg/ml to 10.8 l
645 cm/h
0% to 100% 0 CV, 100% 5 CV
2 min
(C)
200
4000
3000
A280
100
Re-equilibration
CIP
1000
Elution
2000
Wash
50
150
50
100
150
0
0
20
40
60
Time (min)
80
100
Fig 3.39. A 200-fold scale up of a-chymotrypsin on Capto S packed in (A) Tricorn 5/100, (B) XK 16/40 and,
(C) AxiChrom columns.
Intermediate purification of insulin

Capto SP ImpRes was used for intermediate purification where the purpose was to separate
insulin from components remaining from the initial capture step. The resulting chromatogram
is shown in Figure 3.40. Insulin (first peak) was well-resolved from truncated insulin impurities
(middle peak) and C-peptides (third peak). Pooled fractions were analyzed by RPC, which
showed an increase of insulin purity from 64% to 91%. The truncated insulin content was
reduced from 11.5% to 2.8%.
106 11000421 AC
1500
100
150
3000
3000
A280
2500
2000
200
4000
150
Wash
3000
2000
1000
0
0
20
Column:
Medium:
Sample:
Start buffer:
Elution buffer:
Elution:
Tricorn 5/50 CV 1 ml
Capto SP ImpRes
18 mg cleaved insulin*
50 mM acetate, 47.5% ethanol, pH 4
50 mM acetate, 47.5% ethanol, 1 M NaCl, pH 4
First step: 47.5% ethanol, 130 mM NaCl, pH 4 (10 CV)
Second step: 47.5% ethanol, 1 M NaCl, pH 4 (5 CV)
Residence time:
2.5 min
* Kindly provided by Biomm S.A. (Brazil).
Desthreonine/desamido-insulin
900
Pooled fractions
800
100
C-peptide
90
80
70
A280 (mAU)
600
60
500
50
400
40
300
30
200
20
100
10
700
0
0
10
20
30
Volume (ml)
40
50
Fig 3.40. The intermediate step purification of insulin on Capto SP ImpRes removes contaminants such as
desthreonine- and desamido-insulin.
Polishing of MAb
To evaluate Capto S ImpAct for removal of aggregates, four different MAb purified on
MabSelect SuRe medium were run using linear gradient elution in Tricorn columns. Fractions
from the elution peaks were collected and analyzed by analytical SEC for aggregate content.
HCP and protein A content were analyzed using a Gyrolab workstation and a commercial
ELISA assay, respectively. As can be seen in Table 3.24, Capto S ImpAct demonstrates
effective aggregate and HCP removal at a high monomer recovery. Figure 3.45 shows the
chromatogram for MAb E, illustrating that aggregates (green) elute at the tail of the elution
peak. For this MAb, the aggregate level was reduced to 0.6% at 90% monomer recovery.
The initial aggregate content was 2%.
Table 3.24. Results from the purification of four MAb using Capto S ImpAct
MAb A
MAb C
MAb D
MAb E
DBC (mg/ml medium)
108
92
118
122
Load (mg/ml medium)
80
64
80
85
Start aggregate content (%)
Aggregates at 90% monomer recovery (%)
0.9
0.6
1.2
0.6
Start HCP content (ppm)
34
1800
300
454
HCP at 90% monomer recovery (ppm)
42
25
43
Start protein A content (ppm)
<1
Protein A at 90% monomer recovery (ppm)
<1
<1
<1
<1
Elution pool volume (CV)
5.1
5.4
4.0
6.3
Elution pool concentration at 90%

monomer recovery (mg/ml)
13.6
10.6
17.8
12.3
11000421 AC 107
3500
70
200
3000
60
175
2500
50
2000
40
1500
30
1000
20
500
10
25
0
0
20
40
60
Volume (ml)
80
150
125
100
75
50
Capto S ImpAct
Tricorn 5/100, bed height 10 cm
MAb E, purified on MabSelect SuRe medium
85 mg/ml medium
50 mM sodium acetate + 500 mM NaCl, pH 5.3
0.35 ml/min, residence time 5.4 min
Linear, 0 to 350 mM NaCl in 20 CV
Aggregates (%)
mAU
Medium:
Column:
Sample:
Sample load:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
100
Fig 3.41. Chromatogram from purification of MAb E using Capto S ImpAct in a Tricorn 5/100 column.
Histogram in green represents aggregates in fractions. SEC was used for aggregate content analysis,
using a prepacked Superdex 200 Increase 10/300 GL column.
Guidelines for selection of media, buffer, pH and ionic strength conditions and method
and chemicals. Filter solutions using filters of 1 m or less. To avoid formation of air
bubbles in a packed column, maintain buffers and columns at constant temperature
before and during a run.
substance when using an anion exchanger (Q, DEAE) and 0.5 to 1.0 pH unit below the pI
of the target substance when using a cation exchanger (S, SP).
Anion exchange (Q)
Start buffer:
Elution buffer:
20 mM Tris-HCl, 1 M NaCl, pH 8.0
Cation exchange (SP)

Start buffer:
Elution buffer:
or
Start buffer:
Elution buffer:
108 11000421 AC

50 mM 2-(N-Morpholino)ethanesulfonic acid (MES), pH 6.0

Flow rates: 1 ml/min (HiTrap 1 ml), 5 ml/min (HiTrap 5 ml), 1.2 ml/min (HiScreen 4.7 ml).
1. Remove the stopper and connect the column to the system (or syringe) with a
drop-to-drop connection to avoid introducing air into the column.
2. Remove the snap-off end at the column outlet and wash with 1 column volume (CV)
of distilled water. This step ensures removal of ethanol and avoids the precipitation of
buffer salts upon exposure to ethanol. The step can be omitted if precipitation is not
likely to be a problem.
3. Wash with 5 CV of start buffer.
4. Wash with 5 CV of elution buffer.

Linear ionic strength gradients should always be used for method development or when
starting with an unknown sample. Linear ionic strength gradients are easy to prepare and very
reproducible when generated by a suitable chromatography system. The results obtained can
then serve as a base from which to optimize the separation.
1. Equilibrate the column with 5 to 10 CV of start buffer or until the UV baseline, eluent pH,
and conductivity are stable.
2. Adjust the sample to the chosen starting pH and conductivity and apply to the column.
3. Wash with 5 to 10 CV of start buffer or until no material appears in the effluent.
4. Begin elution using a gradient volume of 10 to 20 CV and an increasing salt
concentration up to 500 mM NaCl (50% elution buffer).
5. Wash with 5 CV of 1 M NaCl (100% elution buffer) to elute any remaining ionically
bound material.
6. Re-equilibrate with 5 to 10 CV of start buffer or until the UV baseline, eluent pH, and
conductivity reach the required values.

Reduce separation time and buffer consumption by transferring to a step elution.
1. Equilibrate the column with 5 to 10 CV of start buffer until the UV baseline, eluent pH,
and conductivity are stable.
2. Adjust the sample to the chosen starting pH and conductivity and apply to the column.
3. Wash with 5 to 10 CV of start buffer or until no material appears in the effluent.
4. Elute the target protein with 5 CV of start buffer including NaCl at chosen concentration.
5. If necessary: repeat step 4 at higher NaCl concentrations until the target protein has
been eluted.
7. Re-equilibrate with 5 to 10 CV of start buffer or until the UV baseline, eluent pH, and
conductivity reach the required values.
11000421 AC 109
Save time by using higher flow rates during the high salt wash and re-equilibration steps.
Do not exceed the maximum recommended flow and back pressure for the column.
Cleaning
Correct preparation of samples and buffers, including a high salt wash (1 to 2 M NaCl) after
each purification, should maintain columns in good condition. However, reduced performance,
increased back pressure or blockage indicates that the medium needs cleaning.

4. Rinse with at least 2 CV of distilled water.
5. Wash with at least 5 CV of start buffer until eluent pH and conductivity have reached
Appendix 1.
Chemical stability
For daily use, Capto media are stable in all common, aqueous buffers, 1 M NaOH, denaturing
agents (8 M urea, 6 M guanidine hydrochloride), 70% ethanol, 30% acetonitrile, and with
additives such as nonionic detergents.
Avoid cationic detergents with Capto S, Capto SP ImpRes, and Capto S ImpAct.
Avoid anionic detergents with Capto Q and Capto Q ImpRes.
Avoid oxidizing agents.
Storage
Wash with 2 CV of distilled water followed by 2 CV of 20% ethanol (Capto Q, Capto DEAE,
Capto Q ImpRes) or 20% ethanol containing 200 mM sodium acetate (Capto S, Capto SP ImpRes,
Capto S ImpAct). Store at 4C to 30C. Do not freeze. Ensure that the column is sealed well to
avoid drying out.
Capto media with multimodal functionality

Some Capto media have ligands with multimodal functionality, where the ligand interacts with
the target protein through two or more modes of action. This multimodal functionality gives
a different selectivity compared to standard ion exchangers, which allows multimodal ion
exchangers a wider window of operation in circumstances where traditional media are not as
effective as desired. Such circumstances can be encountered, for example, when the loading
conductivity of the sample is too high for traditional IEX media, when there is a need to reduce
the number of purification steps, or when the selectivity of traditional media is insufficient
to provide the required purity of the target protein. See the Multimodal Chromatography
Handbook, 29054808 for more information about our multimodal Capto media.
110 11000421 AC
Chapter 4
Ion exchange in a Purification Strategy (CIPP)
To ensure efficient, reproducible purification giving the required degree of purity, it is beneficial
to develop a multistep process using the purification strategy of Capture, Intermediate
Purification, and Polishing (CIPP), shown in Figure 4.1.
CIPP is used in both the pharmaceutical industry and in the research laboratory to ensure faster
method development, a shorter time to pure product and good economy. This chapter gives a
brief overview of this approach which is recommended for any multi-step protein purification.
The Strategies for Purification Handbook from GE is a definitive guide for planning efficient and
effective protein purification strategies. An important first step for any purification is correct
sample preparation and this is covered in more detail in Appendix 1 and Chapter 2.
IEX plays a significant and highly flexible role in most multistep purification schemes. If a
specific affinity medium is not available or if little is known about the target molecule, IEX is
recommended as the first step to consider for any purification. The technique can be used
for capture, intermediate purification, or polishing, according to the demands of the specific
application. Since IEX offers different selectivities (using anion or cation exchangers) and since
the pH of the purification can be modified to alter the charge characteristics of the sample
components, it is possible to use the technique more than once in the same purification scheme.
In addition, IEX can be used with step elution for a rapid capture step or with gradient elution to
achieve the highest resolution in a polishing step.
Polishing
Achieve final high-level purity
Purity
Remove bulk impurities
Capture
Isolate, concentrate, and stabilize
Preparation, extraction, clarification

Step
Fig 4.1. Preparation and CIPP.
Applying CIPP
Imagine the purification has three phases: Capture, Intermediate Purification, and Polishing.
Assign a specific objective to each step within the purification process.
The issues associated with a particular purification step will depend greatly upon the
properties of the starting material. Thus, the objective of a purification step will vary according
to its position in the process.
11000421 AC 111
In the capture phase, the objectives are to isolate, concentrate, and stabilize the target product.
The product should be concentrated and transferred to an environment that will conserve
potency/activity.
During the intermediate purification phase, the objectives are to remove most of the bulk
impurities, such as other proteins and nucleic acids, endotoxins, and viruses.
In the polishing phase, most impurities have already been removed. The objective is to achieve
final purity by removing any remaining trace impurities or closely related substances.
The optimal selection and combination of purification techniques for Capture, Intermediate
Purification, and Polishing is crucial for an efficient purification.
CIPP does not mean that there must always be three purification steps. For example,
capture and intermediate purification might be achievable in a single step, as might
intermediate purification and polishing. Similarly, purity demands can be so low that
a rapid capture step is sufficient to achieve the desired result. For purification of
therapeutic proteins, a fourth or fifth purification step might be required to fulfill the
highest purity and safety demands. The number of steps used will always depend upon
the purity requirements and intended use of the protein.
Selection and combination of purification techniques

Proteins are purified using purification techniques that separate according to differences in
specific properties, as shown in Table 4.1.
Table 4.1. Protein properties used during purification
Protein property
Technique
Size
Size exclusion chromatography (SEC)
Charge
Ion exchange chromatography (IEX)
Hydrophobicity
Hydrophobic interaction chromatography (HIC),

Reversed phase chromatography (RPC)
Biorecognition (ligand specificity)
Affinity chromatography (AC)
There are four important performance parameters to consider when planning each purification
step: resolution, capacity, speed, and recovery. Optimization of any one of these four
parameters can be achieved only at the expense of the others, and each purification step will
be a compromise (Fig. 4.2). The importance of each parameter will vary depending on whether
a purification step is used for capture, intermediate purification, or polishing. Purification
methods should be selected and optimized to meet the objectives for each purification step.
Resolution
Speed
Recovery
Capacity
Fig 4.2. Key performance parameters for protein purification. Each purification step should be optimized
for one or two of the parameters.
112 11000421 AC
Capacity, in the simple model shown, refers to the amount of target protein loaded during
purification. In some cases the amount of sample that can be loaded will be limited by volume (as
in SEC) or by large amounts of contaminants rather than the amount of the target protein.
Speed is most important at the beginning of purification where contaminants such as
proteases must be removed as quickly as possible.
Recovery becomes increasingly important as the purification proceeds because of the
increased value of the purified product. Recovery is influenced by destructive processes in
the sample and by unfavourable conditions on the column.
Resolution is achieved by the selectivity of the technique and the efficiency and selectivity of
the chromatography matrix in producing narrow peaks. In general, resolution is most difficult
to achieve in the final stages of purification when impurities and target protein are likely to
have very similar properties.
Select a technique to meet the objectives for the purification step.
Choose logical combinations of purification techniques based on the main benefits of
the technique and the condition of the sample at the beginning or end of each step.
A guide to the suitability of each purification technique for the stages in CIPP is shown in Table 4.2.
Table 4.2. Suitability of purification techniques for CIPP
Typical
characteristics
Purification
phase
Resolution
Capacity
Capture
Intermediate
Polishing
AC
+++
or
++
+++
or
++
+++
++
Various binding conditions
Specific elution conditions
IMAC
+++
++
+++
++
Low concentration of
imidazole, pH > 7.0
High concentration of
imidazole, 500 mM NaCl,
pH > 7.0
SEC
++
+++
Most conditions acceptable, limited sample volume
Buffer exchange possible,

diluted sample
IEX
+++
+++
+++
+++
+++
Low ionic strength.

pH depends on protein
and IEX type
High ionic strength or pH

changed
HIC
+++
++
++
+++
+++
High ionic strength,

addition of salt required
Low ionic strength
RPC
+++
++
++
Ion-pair reagents and

organic modifiers might
be required
Organic solvents (risk for

loss of biological activity)
Method
Sample start
conditions
Sample end
conditions
Minimize sample handling between purification steps by combining techniques to avoid

the need for sample conditioning. The product should be eluted from the first column in
conditions suitable for the start conditions of the next column (see Table 4.2).
Ammonium sulfate, often used for sample clarification and concentration (see Appendix
1), leaves the sample in a high salt environment. Consequently HIC, which requires high
salt to enhance binding to the media, becomes the excellent choice as the capture
step. The salt concentration and the total sample volume will be significantly reduced
after elution from the HIC column. Dilution of the fractionated sample or rapid buffer
exchange using a desalting column will prepare it for the next IEX or AC step.
11000421 AC 113
SEC is a nonbinding technique unaffected by buffer conditions, but with limited volume
capacity. SEC is well-suited for use after any of the concentrating techniques (IEX, HIC,
AC) since the target protein will be eluted in a reduced volume and the components
from the buffer will not affect the size exclusion process.
Selection of the final strategy will always depend upon specific sample properties and the
required level of purification. Logical combinations of techniques are shown in Figure 4.3.
(NH4)2SO4 precipitation
Capture
AC
AC
HIC
HIC
AC
IEX
IEX
HIC
HIC
IEX
IEX
SEC
GF
SEC
GF
SEC
Intermediate
Polishing
SEC or
IEX
Fig 4.3. Examples of logical combinations of chromatography steps.
For any capture step, select the technique showing the most effective binding to
the target protein while binding as few of the contaminants as possible, that is, the
technique with the highest selectivity and/or capacity for the target protein.
A sample is purified using a combination of techniques and alternative selectivities. For
example, in an IEX-HIC-SEC strategy, the capture step selects according to differences in
charge (IEX), the intermediate purification step according to differences in hydrophobicity (HIC),
and the final polishing step according to differences in size (SEC).
If nothing is known about the target protein, use IEX-HIC-SEC. This combination of
techniques can be regarded as a standard protocol.
Consider the use of both anion and cation exchange chromatography to give different
selectivities within the same purification strategy.
114 11000421 AC
Ion exchange as a capture step

When IEX is used as a capture step, the objective is to quickly adsorb the protein(s) of interest
from the crude sample and isolate them from critical contaminants such as proteases and
glycosidases. The target protein(s) are concentrated and transferred to an environment which
will conserve potency/activity. Removal of other critical contaminants may also be achieved by
careful optimization of pH and elution conditions.
The focus is on capacity and speed in a capture step. It is advisable to compromise on the
potential resolution that can be achieved by an IEX separation in order to maximize the
capacity and/or speed of the separation in this first step.
IEX media for capture steps should offer high speed and high capacity. The choice of a suitable
IEX medium depends on the sample properties and the scale of the purification (see also
Chapter 5, Large-scale purification). Examples of IEX capture media include:
1. Sepharose Fast Flow (90 m particle size) good resolution for crude mixtures at any scale
using flow velocities up to 300 cm/h and offering a wide range of selectivities.
2. Capto (90 m particle size) - excellent pressure-flow properties for large-scale applications
using flow velocities up to 700 cm/h.
3. Sepharose XL (90 m particle size) high capacity, good resolution for capture of selected
proteins at laboratory and process scale using flow velocities up to 300 cm/h.
4. Sepharose Big Beads (200 m particle size) for viscous samples that preclude the use of
IEX media with smaller particle size, using flows up to 300 cm/h, or for fast separations of
very large sample volumes when resolution is of less importance, using flows up to 1000 cm/h.
If only milligram quantities of product are needed and the capture step will not be scaled up,
use high-performance media such as SOURCE or Sepharose High Performance according to
the capacity required.
Select start conditions that avoid adsorption of contaminants and so help to maximize
the binding capacity for the target protein(s). This will facilitate a fast, simple step
elution of the concentrated target protein(s).
11000421 AC 115
Capture using Sepharose Q XL

Figure 4.4 shows optimization of a capture step used for purification of a recombinant enzyme,
deacetooxycephalosporin C synthase (DAOCS). Since this enzyme is oxygen-sensitive, it was
important to rapidly remove the most harmful contaminants from the relatively unstable target
protein. The isoelectric point of DAOCS (pI = 4.8) made an anion exchanger the most suitable
choice. Columns from the HiTrap IEX Selection Kit were screened to select the most suitable
medium (results not shown) before optimizing the separation on a larger HiPrep Q XL 16/10 column.
After a linear gradient elution (A), a multi-stepwise elution was tested (B). Since this caused a
broader elution peak, it was decided to use a simple stepwise elution (C). In comparison with
the gradient elution, the speed of the purification increased, buffer consumption decreased, and
the target protein was eluted in a smaller volume (note that the x-axes differ between A and C).
Column:
Sample:
Sample volume:
Start buffer:
Elution buffer:
System:
HiPrep Q XL 16/10
Clarified E. coli extract
40 ml
50 mM Tris-HCl, 1 mM EDTA, pH 7.5; 2 mM DTT, 200 mM benzamidine-HCl, 0.2 mM PMSF
Start buffer + 1 M NaCl
10 ml/min (300 cm/h)
KTA system
(B)
(A)
400
3000
A 280 nm
100
80
60
2000
40
1000
20
20
0
0
100
200
Volume (ml)
40
60
200
A 280 nm
80
300
300
0
0
100
Volume (ml)
200
(C)
80
A 280 nm
60
2000
40
1000
20
3000
0
0
0
50
100
150
Volume (ml)
200
Fig 4.4. Capture step using IEX and optimization of conditions. The elution position of DAOCS is shaded.
116 11000421 AC
Ion exchange for intermediate purification

When IEX is used for intermediate purification, the objective is to remove most of the significant
impurities such as proteins, nucleic acids, endotoxins, and viruses.
In a typical intermediate purification step, speed is less critical since sample volume has
been reduced and damaging contaminants have been removed during capture. Focus is on
capacity and resolution in order to maintain productivity (amount of target protein processed
per column in unit time) and to achieve as high selectivity (purity) as possible. Consequently,
a gradient elution will usually be required.
Use a technique with a selectivity that is complementary to that used in the capture step.
IEX media for intermediate purification should offer high capacity and high resolution with
a range of complementary selectivities The choice of a suitable IEX medium depends on the
sample properties and the scale of the purification (see also Chapter 5, Large-scale purification).
Examples of IEX media for intermediate purification:
1. Sepharose High Performance (34 m particle size) high resolution in laboratory scale using
flow velocities up to 150 cm/h.
2. Capto ImpAct and Capto ImpRes (50 m and 40 m particle size) - excellent pressure-flow
properties for large-scale applications using flow velocities up to 200 cm/h.
3. SOURCE 15 (15 m particle size) high throughput, high resolution for laboratory or largescale applications using flow velocities up to 1800 cm/h.
4. SOURCE 30 (30 m particle size) an alternative to SOURCE 15 for large-scale applications
when flow velocities up to 2000 cm/h can be used.
5. Sepharose Fast Flow (90 m particle size) fast separations using flow velocities up to
300 cm/h, broad range of selectivities.
If only milligram quantities are required and the intermediate purification step will not be
scaled-up, use MonoBeads or MiniBeads according to the capacity required.
Optimize the selectivity of the medium to ensure high binding capacity and to maximize
resolution. Use continuous gradient or multistep elution conditions.
11000421 AC 117
Intermediate purification using Capto S ImpAct

Capto S ImpAct was used for intermediate purification in a three-step MAb-purification process (Fig 4.5).
MabSelect SuRe LX
Capto S ImpAct (bind/elute [B/E] mode)
Capto adhere ImpRes (flowthrough [FT] mode)
Fig 4.5. Three-step purification deploying MabSelect SuRe LX for capture, Capto S ImpAct for intermediate
purification, and Capto Q for polishing.
The intermediate purification of MAb A resulted in reduction of aggregate concentration from

2% to 0.6% and host cell protein (HCP) concentration from 1800 ppm to 42 ppm. The yield of
MAb A monomer in this step was 90%.
The high selectivity of Capto S ImpAct between MAb monomer, aggregates, and HCP can be
seen from the chromatograms in Figure 4.6.
Column:
Medium:
Sample:
Load:
Residence time:
Binding buffer:
Wash:
Elution buffer:
System:
Tricorn 5/100
Capto S ImpAct (B/E mode)
MAb A in 50 mM sodium acetate, pH 5.3 (6.8 mS/cm)
64 g MAb/l medium (70% of QB10)
5.4 min
50 mM sodium acetate, pH 5.3 (6.8 mS/cm)
5 CV of binding buffer
50 mM sodium acetate, pH 5.3, 0 to 350 mM NaCl in 20 CV
KTA system
100
5000
4000
80
3000
60
2000
40
1000
20
8000
7000
5000
4000
3000
HCP (ng/ml)
Aggregate (%)
A280 (mAU)
6000
2000
1000
0
0
10
20
30
40
50
Volume (ml)
60
70
80
Fig 4.6. Intermediate purification of MAb A using Capto S ImpAct. Aggregates eluted in the tail of the elution
peak (red histogram), whereas most of the HCP (green histogram) eluted after the elution peak (blue UV trace).
118 11000421 AC
Ion exchange as a polishing step

When IEX is used for polishing, most impurities have been removed except for trace amounts
or closely related substances such as structural variants of the target protein, nucleic acids,
viruses, or endotoxins. The purpose of the separation is to reduce these variants and trace
contaminants to acceptable levels for the application. In contrast to capture steps where a
fast, high capacity, step elution is most commonly used, a polishing step will therefore focus on
achieving the highest possible resolution. An example of this approach is shown
in Figure 4.7 in which Mono S 5/50 GL was used to separate a recombinant DNA binding
protein, transposase TniA, from minor contaminants remaining after partial purification by
anion exchange and heparin affinity chromatography.
Column:
Sample:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
Mono S 5/50 GL
14.5 ml from HiPrep 26/10 Desalting
20 mM MES pH 6.5, 1 mM EDTA, 2 mM MgCl2, 1 mM DTT
20 mM MES pH 6.5, 1 mM EDTA, 2 mM MgCl2, 1 mM DTT, 1 M NaCl
1 ml/min
1200
A 280 nm
1000
800
600
400
200
0
0. 0
10 .0
20.0
Volume (ml)
30 .0
40.0
Fig 4.7. High-resolution cation exchange chromatography on Mono S 5/50 GL. The desalted sample was
applied to Mono S 5/50 GL, and TniA was eluted as a sharp peak at approximately 500 mM NaCl.
IEX media for polishing steps should offer high resolution. The choice of a suitable IEX medium
depends on the sample properties and the scale of the purification (see also Chapter 5, Largescale purification). Examples of IEX polishing media:
1. MiniBeads (3 m particle size) polishing at microscale when highest resolution is essential.
2. MonoBeads (10 m particle size) polishing at laboratory scale when highest resolution is
essential and a higher capacity than MiniBeads is required.
3. SOURCE 15 (15 m particle size) rapid, high resolution polishing for laboratory or largescale applications using flow velocities up to 1800 cm/h.
4. SOURCE 30 (30 m particle size) an alternative to SOURCE 15 for large-scale applications
when flow velocities up to 2000 cm/h can be used.
5. Sepharose High Performance (34 m particle size) high resolution at laboratory scale using
flow velocities up to 150 cm/h.
6. Capto ImpAct and Capto ImpRes (50 m and 40 m particle size) - excellent pressure-flow
properties for large-scale applications using flow velocities up to 200 cm/h.
Optimize the gradient elution to maximize selectivity. Use high efficiency media with
small bead sizes to improve resolution.
11000421 AC 119
Alternative techniques for polishing

Most commonly, separations by charge, hydrophobicity, or affinity will have been used in earlier
stages of a purification strategy so that high-resolution SEC is ideal for the final polishing step.
The product can be purified and transferred into the required buffer in one step and dimers and
aggregates can be removed, as shown in Figure 4.6.
SEC is also the slowest of the chromatography techniques and the size of the column determines
the volume of sample that can be applied. It is therefore most logical to use SEC after techniques
that reduce sample volume so that smaller columns can be used. Media for polishing steps
should offer the highest possible resolution. Superdex Increase is the first choice at laboratory
scale and Superdex prep grade for large-scale applications.
Column:
Sample:
Sample load:
Buffer:
XK 16/60 packed with Superdex 75 prep grade

Partly purified ZZ-brain IGF
1.0 ml
300 mM ammonium acetate, pH 6.0
0.5 ml/min (15 cm/h)
monomeric ZZ-Brain IGF
A 280 nm
0.01
0.005
Vo
0
0
Fraction 1
Vt
2
2
Time (h)
Fig 4.6. Final polishing step: separation of dimers and multimers on Superdex 75 prep grade.
RPC can also be considered for a polishing step, provided that the target protein can withstand
the run conditions. RPC separates proteins and peptides on the basis of hydrophobicity and
is a high selectivity (high resolution) technique, usually requiring the use of organic solvents.
The technique is widely used for purity check analyses when recovery of activity and tertiary
structure are not essential. Since many proteins are denatured by organic solvents, RPC is
not generally recommended for protein purification because recovery of activity and return
to a correct tertiary structure can be compromised. However, in the polishing phase, when
the majority of protein impurities have been removed, RPC can be an excellent technique,
particularly for small target proteins that are not often denatured by organic solvents.
120 11000421 AC
Chapter 5
Large-scale purification
The BioProcess chromatography media family includes media widely used by biopharmaceutical
manufacturers. Support for these products comprises of validated manufacturing methods,
secure long-term chromatography media supply, safe and easy handling, and regulatory
support files (RSF) to assist process validation and submissions to regulatory authorities. In
addition, the Fast Trak Training and Education team provides high-level hands-on training for
all key aspects of bioprocess development and manufacturing.
All BioProcess media have high chemical stability to allow efficient cleaning/sanitization
procedures and validated packing methods established for a wide range of large-scale columns.
BioProcess media for IEX

BioProcess media for ion exchange chromatography are designed for large scale purification
and use in industrial processes. Examples of BioProcess media for IEX purification are shown
in Table 5.1 (the properties and handling of each medium are described in detail in Chapter 3).
Most of the media, except Sepharose Big Beads, are available in HiTrap and HiScreen formats
for development of efficient and robust purification parameters before scaling up. Some of
the media are also available in high-throughput process development (HTPD) formats, such
as PreDictor 96-well filter plates for fast and easy parallel screening of running conditions
and PreDictor RoboColumn (miniature columns for use with a robotic station) for testing of, for
example, DBC. By using these small-scale formats in the early stages of process development,
valuable time is saved and buffer and sample consumption reduced.
The range of BioProcess media includes capture media such as Capto, Sepharose Fast Flow,
and Sepharose XL. These media can be used at high flow rates and have high dynamic binding
capacities. Media with smaller beads, such as Capto ImpRes, Capto ImpAct, Sepharose High
Performance, and SOURCE give high final resolution and are suitable for polishing purification
(see also Chapter 4 for the principle of capture and polishing purification).
11000421 AC 121
Table 5.1. Examples of BioProcess chromatography media for IEX
Medium
Chromatography
method
Average
particle size,
d50V (m)
Protein
Recommended binding
flow rate1
capacity1
Main
usage
Strong anion
200
High
low
Capture
Strong cation
200
High
low
Capture
Capto Q
Strong anion
90
High
High
Capture
Capto DEAE
Weak anion
90
High
Medium
Capture
Capto S
Strong cation
90
High
High
Capture
Strong anion
90
Medium
Medium
Capture
Weak anion
90
Medium
Medium
Capture

(high sub)
Weak anion
90
Medium
Medium
Capture
Strong cation
90
Medium
Medium
Capture
Weak cation
90
Medium
Medium
Capture
Q Sepharose XL
Strong anion
90
Medium
High
Capture
SP Sepharose XL
Strong cation
90
Medium
High
Capture
Capto Q ImpRes
Strong anion
40
Medium
Medium
Polishing
Capto SP ImpRes
Strong cation
40
Medium
Medium
Polishing
Capto S ImpAct
Strong cation
50
Medium
High
Polishing
SOURCE 30Q
Stong anion
30
High
Medium
Polishing
SOURCE 30S
Strong cation
30
High
Medium
Polishing
SOURCE 15Q
Strong anion
15
High
Medium
Polishing
SOURCE 15S
Strong cation
15
High
Medium
Polishing
Recommended flow rate and protein binding capacity are expressed as high, medium, or low for easy comparison. The
values for each medium can be found in Chapter 3.
Capture purification
General capture purification is performed using Capto and Sepharose Fast Flow. When IEX
is used as a capture step, the objective is to quickly adsorb the protein of interest from the
crude sample and remove critical contaminants such as proteases. For modern industrial
applications, Capto media are usually the preferred option having benefits such as high rigidity
and ability to run at high flow rates. Figure 5.1 shows a comparison of media properties. Capto
media give increased DBC over a wide range of residence times due to excellent mass transfer
properties. Further, a high DBC contributes to shortening the overall processing time as the
total number of cycles can be reduced.
Sepharose Fast Flow media are available with a wide range of ion exchange groups and are
still widely used in biopharmaceutical processes.
122 11000421 AC
(A)
(B)
200
140
Dynamic binding capacity (mg/ml)
160
Capto Q
120
100
80
60
40
20
0
3
4
5
6
Residence time (min)
180
160
Capto S
140
120
100
80
60
40
20
0
3
4
5
6
(C)
200
180
Capto DEAE
160
140
120
100
80
60
40
20
0
3
4
5
6
Fig 5.1. Dynamic binding capacity (DBC) as a function of residence time for Capto and corresponding
Sepharose Fast Flow media. Proteins: (A) BSA; (B) a-chymotrypsin; (C) amyloglucosidase. Residence times
below 2 min are not possible for Sepharose Fast Flow in large-scale columns due to lower pressure/flow
properties than for Capto media.
The capture media Q Sepharose XL and SP Sepharose XL have greater binding capacity
compared with other Sepharose media. The high binding capacity has been obtained by
binding the ionic group to long, flexible dextran chains coupled to the agarose matrix.
Sepharose Big Beads are designed for capture of large volumes of crude and/or viscous sample.
Due to the large bead size of the Sepharose Big Beads matrix (200 m average particle size),
a lower resolution compared with other capture media can be expected.
Polishing purification
The polishing purification is performed using chromatography media with smaller average
bead size, such as Capto ImpRes, Capto ImpAct, and SOURCE media. In contrast to capture
purification where a fast, high-capacity step elution is most commonly used, a polishing
purification will focus on achieving the high resolution (resulting in high purity).
Although the charged groups of the S, SP, Q, and DEAE ligands are identical between
different IEX media, minor differences in selectivity can occur due to differences in base
matrix, ligand density, ligand composition, and surface extenders. Capto ImpRes media are
designed for high resolution and high throughput during polishing steps. A comparison with
Q Sepharose High Performance in HiScreen columns showed similar resolution results, although
HiScreen Capto Q ImpRes was run at 300 cm/htwice the flow velocity of HiScreen Q HP (Fig 5.2).
Capto ImpRes media provide improved performance over Sepharose when scaling up due to
their good pressure/flow properties, allowing high flow rates.
11000421 AC 123
Columns:
Sample:
Start buffer:
Elution buffer:
Gradient:
Residence time:
HiScreen Capto Q ImpRes, HiScreen Q HP, 4.7 ml

5 ml apo-transferrin (0.3 mg/mL), -lactoalbumin (0.4 mg/ml),
soybean trypsin inhibitor (0.6 mg/ml) in start buffer
50 mM Tris, pH 7.4
50 mM Tris, 500 mM NaCl, pH 7.4
HiScreen Capto Q ImpRes, 2.3 ml/min (300 cm/h); HiScreen Q HP, 1.2 ml/min (150 cm/h)
HiScreen Capto Q ImpRes, 2 min; HiScreen Q HP, 4 min
(A) HiScreen Capto Q ImpRes
300
50
200
30
150
20
100
50
0
0
20
40 60 80 100 120
Volume (ml)
50
250
40
200
30
150
20
100
10
50
40
250
A280 (mAU)
300
A280 (mAU)
(B) HiScreen Q HP
10
20
40 60 80 100 120
Volume (ml)
Fig 5.2. Chromatograms from resolution comparisons on two IEX media with the same Q charged group
ligand. Peaks (left to right) are apo-transferrin, -lactoalbumin, and soybean trypsin inhibitor. The small
bead size of (A) Capto Q ImpRes and (B) Q Sepharose High Performance gives high resolution in both cases.
However, the higher flow velocity possible with Capto Q ImpRes makes it a good choice for large-scale
intermediate purification or polishing.
The difference between Capto ImpRes and Sepharose High Performance media is also
illustrated in Figure 5.3. Although the bead sizes of the media are similar, the pressure/flow
properties of Capto ImpRes are significantly improved as a result of the greater mechanical
stability of its high-flow base matrix.
500
Capto SP ImpRes
Velocity (cm/h)
400
300
200
100
0
0
2
3
Pressure (bar)
Fig 5.3. The pressure-flow properties of Capto ImpRes are enhanced compared with
Sepharose High Performance due to the improved mechanical stability of the base matrix.
Running conditions: AxiChrom 300 column, 20 cm bed height with water at 20C.
124 11000421 AC
Capto S ImpAct chromatography medium is designed for the polishing steps of MAb and a wide
range of other biomolecules. In this study, the binding capacity for MAb A and the efficiency
in the clearance of impurities was evaluated. The content of aggregates in the sample was
approximately 7% after the initial protein A capture step. A high load, 80 mg/ml medium, was
applied to the Capto S ImpAct column and elution was performed using a linear gradient. The
chromatogram illustrates that aggregates (green) elute at the tail of the elution peak (Fig 5.4).
The purification resulted in 90% monomer recovery and reduction of aggregate content to 0.9%.
Column:
Sample:
Sample load:
Start buffer:
Elution buffer:
Flow rate loading:
Flow rate elution:
Gradient:
HiScreen Capto S ImpAct, CV 4.7 ml

~ 10 mg/mL MAb A purified on MabSelect SuRe, buffer exchanged into start buffer
80 mg/ml medium
50 mM sodium acetate, pH 5.0 + 50 mM NaCl
50 mM sodium acetate, pH 5.0 + 500 mM NaCl
1.1 ml/min, residence time 4 min
0.6 ml/min, residence time 8 min
Linear, 20 CV
175
2500
60
150
2000
50
40
1500
30
1000
500
0
0
20
40
60
80
100 120 140

Volume (ml)
160
180
200
Aggregates (%)
mAU
70
125
100
75
20
50
10
25
200
3000
220
Fig 5.4. Purification of MAb A at a high sample load (80 mg/ml medium). Histogram in green represents
aggregates in fractions.
SOURCE 30Q and 30S are easy to pack at both laboratory and large scale and are suitable for
industrial processes when large volumes of partially purified material need to be processed.
The excellent scalability of SOURCE 30S was shown in a scale up from a 105-ml small
scale-column to a 50-l custom-designed production column (Fig 5.5). The results show that
performance was maintained despite high flow rates and an almost 500-fold scale-up factor.
11000421 AC 125
Column:
Sample:
Sample load:
Start buffer:
Elution buffer:
Flow rate:
Gradient:
(A)
SOURCE 30S: (A) FineLINE Pilot 35, 35 mm i.d. 109 mm (105 ml)
SOURCE 30S: (B) FineLINE 100, 100 mm i.d. 100 mm (0.78 l)
SOURCE 30S: (C) FineLINE 800, 800 mm i.d. 100 mm (50 l)
Ribonuclease A, cytochrome C, and lysozyme (3.75:1:1)
0.32 mg total protein/ml media
20 mM sodium phosphate + 400 mM NaCl, pH 6.8
(A) 48 ml/min (B) 0.39 l/min, (C) 25 l/min
(B)
0.040
0.040
0.080
0.030
0.080
A 280 nm
A 280 nm
0.030
0.060
A280 nm
A280 nm
0.020
0.020
0.010
0.060
0.040
0.040
0.020
0.010
0.020
0.000
0.000
0.000 1000
1500
2000
2500
1000
1500
Volume
2000(ml)
2500
0.000
10
10
Volume (ml)
15
Volume (l)
15
Volume (l)
20
20
(C)
50
50
AUFSAUFS
40
40
30
30
20
20
10
10
600
800
600
800
1000
Volume
1000 (l)
1200
1400
1200
1400
Volume (l)
Fig 5.5. Scale-up from a FineLINE
Pilot 35 column via FineLINE 100 column (7-fold) to FineLine 800
custom-designed column (64-fold). Total scale-up factor: 476-fold.
SOURCE 15Q and SOURCE 15S have a uniform, 15 m diameter, spherical shape and are
designed for high-resolution purification at lab scale and for scaling up. The beads give stable
packed beds with low back pressure. Figure 5.6 illustrates the maintained performance of
high-resolution separations also at very high flow rates.
Chymotrypsinogen, cytochrome C
Resolution (Rs)
Cytochrome C, lysozyme
2
200
40
600
14
1000
4
Separation time (min)
1400
1800
Fig 5.6. Resolution vs flow velocity for model proteins. Column: RESOURCE S, 1 ml (6.4 mm diameter
30 mm bed height). Sample: chymotrypsinogen, cytochrome C, lysozyme. Total load 16 mg.
126 11000421 AC
Prepacked, disposable solutions speed up the downstream process

In addition to a wide range of industrial-scale columns such as AxiChrom columns and bulk
media for purification of proteins, GE offers large-scale, disposable ReadyToProcess columns.
These columns are prepacked, prequalified, and presanitized process chromatography
columns available with a range of BioProcess mediaincluding Capto, Capto ImpAct,
Capto ImpRes, Sepharose Fast Flow, and Sepharose High Performance product families.
ReadyToProcess columns are available in several different sizes (Fig 5.7) and are designed
for purification of biopharmaceuticals (e.g., proteins and antibodies, vaccines, plasmids, and
viruses) for clinical phase I and II studies. Depending on the scale of operations, the columns
can also be used for manufacturing, as well as preclinical studies. ReadyToProcess columns
make column packing, qualification, and sanitization redundant in the purification process
allowing significant time savings.
Fig 5.7. ReadyToProcess columns are easily connected to the system and can be disposed after
completed production.
Custom Designed Media

Custom Designed Media (CDM) can be produced for specific industrial process separations
when suitable media are not available from the standard range. The Custom Designed Media
group (CDM group) works in close collaboration with the user to design, manufacture, test, and
deliver media for specialized purification requirements.
See also Handbook of Process Chromatography: Optimization, Scale-up, and
Validation, 18112156.
11000421 AC 127
128 11000421 AC
Appendix 1
Sample preparation
Samples for chromatographic purification should be clear and free from particulate matter.
Simple steps to clarify a sample before beginning purification will avoid clogging the column, reduce
the need for stringent washing procedures, and extend the life of the chromatographic medium.
Sample extraction procedures and the selection of buffers, additives, and detergents are
determined largely by the source of the material, the stability of the target molecule, the
chromatographic techniques that will be employed and the intended use of the product.
These subjects are dealt with in general terms in the Strategies for Protein Purification
Handbook and more specifically according to target molecule in the Recombinant Protein
Purification Handbook, and Antibody Purification Handbook, available from GE.
Sample stability
In the majority of cases, biological activity needs to be retained after purification. Retaining
the activity of the target molecule is also an advantage when following the progress of
the purification, since detection of the target molecule often relies on its biological activity.
Denaturation of sample components often leads to precipitation or enhanced nonspecific
adsorption, both of which will impair column function. Hence there are many advantages to
checking the stability limits of the sample and working within these limits during purification.
Proteins generally contain a high degree of tertiary structure, kept together by van der Waals
forces, ionic and hydrophobic interactions, and hydrogen bonding. Any conditions capable of
destabilizing these forces may cause denaturation and/or precipitation. By contrast, peptides
contain a low degree of tertiary structure. Their native state is dominated by secondary
structures, stabilized mainly by hydrogen bonding. For this reason, peptides tolerate a much
wider range of conditions than proteins. This basic difference in native structures is also
reflected in that proteins are not easily renatured, while peptides often renature spontaneously.
It is advisable to perform some stability tests before beginning to develop a purification
protocol. The list below shows examples of such testing:
Test pH stability in steps of one pH unit between pH 2.0 and pH 9.0.
Test salt stability with 0 to 2 M NaCl and 0 to 2 M (NH4)2SO4 in steps of 0.5 M.
Test the stability towards acetonitrile and methanol in 10% steps between 0% and 50%.
Test the temperature stability in 10C steps from 4C to 40C.
Test the stability and occurrence of proteolytic activity by leaving an aliquot of the sample
at room temperature overnight. Centrifuge each sample and measure activity and UV
absorbance at 280 nm in the supernatant.
Sample clarification
Centrifugation and filtration are standard laboratory techniques for sample clarification and
are used routinely when handling small samples.
It is highly recommended to centrifuge and filter samples immediately before
chromatographic purification.
11000421 AC 129
Centrifugation
Centrifugation removes lipids and particulate matter, such as cell debris. If the sample is still
not clear after centrifugation, use filter paper or a 5 m filter as a first step and one of the filters
below as a second-step filter.
For small sample volumes or proteins that adsorb to filters, centrifuge at 10 000 g for 15 min.
For cell lysates, centrifuge at 40 000 to 50 000 g for 30 min.
Serum samples can be filtered through glass wool after centrifugation to remove
remaining lipids.
Filtration
Filtration removes particulate matter. Whatman syringe filters, which give the least amount
of nonspecific binding of proteins, are composed of cellulose acetate (CA), regenerated
cellulose (RA), or polyvinylidene fluoride (PVDF) (Table A1.1).
Table A1.1. Whatman syringe filters for filtration of samples
Filter pore size (m)
Up to sample volume (ml)
Whatman syringe filter1 Membrane
0.8
100
Puradisc FP 30
CA
0.45
Puradisc 4
PVDF
0.45
10
Puradisc 13
PVDF
0.45
100
Puradisc 25
PVDF
0.45
10
SPARTAN 13
RC
0.45
100
SPARTAN 30
RC
0.45
100
Puradisc FP 30
CA
0.2
Puradisc 4
PVDF
0.2
10
Puradisc 13
PVDF
0.2
100
Puradisc 25
PVDF
0.2
10
SPARTAN 13
RC
0.2
100
SPARTAN 30
RC
0.2
100
Puradisc FP 30
CA
The number indicates the diameter (mm) of the syringe filter.
For sample preparation before chromatography, select a filter pore size in relation to the bead
size of the chromatographic medium (Table A1.2).
Table A1.2. Selecting a sample filter based on the bead size of the chomatographic medium used
Nominal pore size of filter (m)
Particle size of chromatographic medium (m)
1.0
90 and upwards
0.45
30 or 34
0.22
3, 10, 15 or when extra clean samples or sterile filtration is required
Check the recovery of the target protein in a test run. Some proteins adsorb
nonspecifically to filter surfaces.
130 11000421 AC
Desalting
Desalting columns are suitable for any sample volume and will rapidly remove low molecular
weight contaminants in a single step at the same time as transferring the sample into the
correct buffer conditions. Centrifugation and/or filtration of the sample before desalting is still
recommended. Detailed procedures for buffer exchange and desalting are given in the section
Buffer exchange and desalting later in this appendix.
At laboratory scale, when samples are reasonably clean after filtration or centrifugation,
the buffer exchange and desalting step can be avoided. For affinity chromatography or
hydrophobic interaction chromatography, it might be sufficient to adjust the pH of the sample.
For IEX, it might be sufficient to dilute the sample to reduce the ionic strength.
Specific sample preparation steps

Specific sample preparation steps might be required if the crude sample is known to contain
contamininants such as lipids, lipoproteins, or phenol red that might build up on a column.
Gross impurities, such as bulk protein, should be removed before any chromatographic step.
Fractional precipitation
Fractional precipitation is occasionally used at laboratory scale to remove gross impurities
from the sample. Precipitation techniques separate fractions by the principle of differential
solubility. Because proteins differ in their degree of hydrophobicity, increased salt
concentrations can enhance hydrophobic interactions between the proteins and cause
precipitation. Fractional precipitation can be applied to remove gross impurities in three
different ways, as shown in Figure A1.1.
Clarification
Bulk proteins and particulate
matter precipitated
Extraction, Clarification, Concentration

Target protein precipitated
with proteins of similar solubility
Extraction, Clarification
Bulk proteins and particulate
matter precipitated
Supernatant
Redissolve pellet1
Chromatography
Note: if precipitating agent is
incompatible with next purification step,
use Sephadex G-25 for desalting and
buffer exchange, for example,
HiTrap Desalting or PD-10 columns
Concentration
Target protein
precipitated
with proteins of
similar solubility
Redissolve pellet1
Remember: not all proteins are easy to redissolve, yield can be reduced
Fig A1.1. Three ways to use precipitation.
Precipitation techniques can be affected by temperature, pH, and sample

concentration. These parameters should be controlled to ensure reproducible results.
Examples of precipitation agents are reviewed in Table A1.3. The most common precipitation
method using ammonium sulfate is described in more detail.
11000421 AC 131
Table A1.3. Examples of precipitation techniques

Precipitation agent
Typical conditions for use Sample type
Comment
Ammonium sulfate
As described below.
Stabilizes proteins, no
denaturation, supernatant
can go directly to HIC.
Helps to reduce lipid content.
Dextran sulfate
Add 0.04 ml 10% dextran Samples with high

levels of lipoprotein,
sulfate and 1 ml of
1 M CaCl2 per ml sample, e.g., ascites.
mix 15 min, centrifuge
10 000 g, discard pellet.
Precipitates lipoprotein.
Polyvinylpyrrolidine
Add 3% (w/v), stir 4 h,

centrifuge 17 000 g,
discard pellet.
Samples with high

levels of lipoprotein,
e.g., ascites.
Alternative to dextran sulfate.
Polyethylene glycol
(PEG, Mr > 4000)
Up to 20% w/v.
Plasma proteins.
No denaturation,
supernatant goes directly
to IEX or AC, complete
removal might be difficult.
Stabilizes proteins.
Acetone (cold)
Up to 80% v/v at
0C. Collect pellet
after centrifugation
at full speed in a
microcentrifuge.
Can denature protein

irreversibly.
Useful for peptide
precipitation or
concentration of sample
for electrophoresis.
Polyethyleneimine
0.1% w/v.
Precipitates aggregated
nucleoproteins.
Protamine sulfate
1% w/v.
Precipitates aggregated
nucleoproteins.
Streptomycin sulfate
1% w/v.
Precipitation of nucleic acids.
Caprylic acid
(X/15) g where X =
volume of sample.
> 1 mg/ml proteins

especially immunoglobulins.
Antibody concentration Precipitates bulk of proteins

should be > 1 mg/ml.
from sera or ascites, leaving
immunoglobulins in solution.
Details taken from: Scopes R. K., Protein Purification, Principles and Practice, Springer, (1994), J. C. Janson and L. Rydn, Protein
Purification, Principles, High Resolution Methods and Applications, second ed. Wiley Inc, (1998). Personal communications.
Ammonium sulfate precipitation

Some proteins can be damaged by ammonium sulfate. Take care when adding
crystalline ammonium sulfate; high local concentrations can cause contamination of
the precipitate with unwanted proteins.
For routine, reproducible purification, precipitation with ammonium sulfate should be
avoided in favor of chromatography.
In general, precipitation is rarely effective for protein concentrations below 1 mg/ml.
Solutions needed for precipitation:
Saturated ammonium sulfate solution (add 100 g ammonium sulfate to 100 ml distilled
water, stir to dissolve).
1 M Tris-HCl, pH 8.0.
Buffer for first purification step.
132 11000421 AC
1. Filter (0.45 m) or centrifuge the sample (10 000 g at 4C).

2. Add 1 part 1 M Tris-HCl, pH 8.0 to 10 parts sample volume to maintain pH.
3. Stir gently. Add ammonium sulfate solution, drop by drop. Add up to 50% saturation1.
Stir for 1 h.
4. Centrifuge 20 min at 10 000 g.
5. Remove supernatant. Wash the pellet twice by resuspension in an equal volume of
ammonium sulfate solution of the same concentration (i.e. a solution that will not
redissolve the precipitated protein or cause further precipitation). Centrifuge again.
6. Dissolve pellet in a small volume of the buffer to be used for the next step.
7. Ammonium sulfate is removed during clarification/buffer exchange steps with
Sephadex G-25, using desalting columns (see Buffer exchange and desalting later
in this appendix).
1
The percent saturation can be adjusted either to precipitate a target molecule or to precipitate contaminants.
The quantity of ammonium sulfate required to reach a given degree of saturation varies
according to temperature. Table A1.4 shows the quantities required at 20C.
Table A1.4. Quantities of ammonium sulfate required to reach given degrees of saturation at 20C
Final percent saturation to be obtained
20
25
Starting
percent
saturation
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Amount of ammonium sulfate to add (gram) per liter of solution at 20C
113 144 176 208 242 277 314 351 390 430 472 516 561 608 657 708 761
85
115 146 179 212 246 282 319 358 397 439 481 526 572 621 671 723
10
57
86
117 149 182 216 251 287 325 364 405 447 491 537 584 634 685
15
28
58
88
20
29
59
89
121 154 188 223 260 298 337 378 421 465 511 559 609
29
60
91
123 157 191 228 265 304 344 386 429 475 522 571
30
61
92
125 160 195 232 270 309 351 393 438 485 533
30
62
94
128 163 199 236 275 316 358 402 447 495
31
63
96
130 166 202 241 281 322 365 410 457
31
64
98
132 169 206 245 286 329 373 419
32
65
99
135 172 210 250 292 335 381
33
66
101 138 175 215 256 298 343
33
67
34
69
105 143 183 224 267
34
70
35
72
110 149 190
36
73
112 152
37
75
114
37
76
38
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
119 151 185 219 255 293 331 371 413 456 501 548 596 647
103 140 179 219 261 305

107 146 186 228
11000421 AC 133
Resolubilization of protein precipitates

Many proteins are easily resolubilized in a small amount of the buffer to be used in the next
chromatographic step. However, a denaturing agent may be required for less soluble proteins.
Specific conditions will depend upon the specific protein. These agents must always be
removed to allow complete refolding of the protein and to maximize recovery of mass and
activity. A chromatographic step often removes a denaturant during purification. Table A1.5
gives examples of common denaturing agents.
Table A1.5. Denaturing agents used for resolubilization of relatively insoluble proteins
Denaturing agent
Typical conditions
for use (molar, M)
Removal/comment
Urea
2 to 8
Remove using Sephadex G-25
Guanidine hydrochloride
3 to 6
Remove using Sephadex G-25
Details taken from: Scopes R. K., Protein Purification, Principles and Practice, Springer, (1994), J. C. Janson and L. Rydn,
Protein Purification, Principles, High Resolution Methods and Applications, second ed. Wiley Inc, (1998) and other sources.
Buffer exchange and desalting

Dialysis is frequently mentioned in the literature as a technique to remove salt or other small
molecules and to exchange the buffer composition of a sample. However, dialysis is generally
a very slow technique, requiring large volumes of buffer. There is also a risk of losing material
during handling or as a result of proteolytic breakdown or nonspecific binding to the dialysis
membranes. A simpler and much faster technique is to use a desalting column, packed
with Sephadex G-25, to perform a group separation between high and low molecular weight
substances. Proteins are separated from salts and other small molecules.
In a fast, single step, the sample is desalted, transferred into a new buffer and low molecular
weight materials are removed.
Desalting columns are used not only to remove low molecular weight contaminants, such as
salt, but also for buffer exchange before or after different chromatographic steps and for the
rapid removal of reagents to terminate a reaction.
Sample volumes up to 30% of the total volume of the desalting column can be processed.
Sample concentration does not influence the separation as long as the concentration of
proteins does not exceed 70 mg/ml when using normal aqueous buffers. The sample should be
fully dissolved. Centrifuge or filter to remove particulate material.
For small sample volumes, it is possible to dilute the sample with the start buffer that is
to be used for chromatographic purification, but cell debris and particulate matter must
still be removed.
Volatile buffers such as 100 mM ammonium acetate or 100 mM ammonium
hydrogen carbonate can be used if it is necessary to avoid the presence of NaCl.
Figure A1.2 shows a typical buffer exchange and desalting separation. The process can be
monitored by following changes in UV absorption and conductivity.
134 11000421 AC
0.30
15
0.25
A280
10
0.15
protein
salt
0.10
0.20
5
0.05
0.00
Time (min)
Fig A1.2. Buffer exchange of mouse plasma (10 ml) on HiPrep 26/10 Desalting.
For laboratory-scale operations, Table A1.6 shows examples of prepacked, ready-to-use

desalting and buffer exchange columns (see Size Exclusion Chromatography Handbook,
18102218, for additional formats).
Table A1.6. Examples of desalting and buffer exchange columns
Column
Sample volume (ml)
Sample elution volume (ml)
PD MiniTrap G-25
0.2 to 0.5
0.1 to 0.5
PD-10 (gravity feed column)
1.5 to 2.5
2.5 to 3.5
HiTrap Desalting, 5 ml
0.25 to 1.5
1.0 to 2.0
HiPrep 26/10 Desalting
2.5 to 15
7.5 to 20
To desalt larger sample volumes:

- Connect up to five HiTrap Desalting 5 ml columns in series to increase the sample volume
capacity, for example, two columns: sample volume 3 ml, five columns: sample volume 7.5 ml.
- Connect up to four HiPrep 26/10 Desalting columns in series to increase the sample volume
capacity, for example two columns: sample volume 30 ml, four columns: sample volume 60 ml.
Even with four columns in series, the sample can be processed in 20 to 30 min, at room
temperature, in aqueous buffers.
Instructions are supplied with each column. Desalting and buffer exchange can take less than
5 min per sample with greater than 95% recovery for most proteins.
Manual desalting with HiTrap Desalting 5 ml using a syringe

1. Fill the syringe with buffer. Remove the stop plug. To avoid introducing air into the
column, connect the column drop to drop to the syringe (via the adapter provided).
2. Remove the snap-off end.
3. Wash the column with 25 ml buffer at 5 ml/min to remove completely the 20% ethanol
(supplied as storage buffer). If air is trapped in the column, wash with degassed buffer
until the air disappears. Air bubbles introduced onto the column by accident during
sample application do not influence the separation.
4. Apply the sample (0.25 to 1.5 ml) using a 2 to 5 ml syringe at a flow rate between 1 to
10 ml/min. Discard the liquid eluted from the column.
5. If the sample volume is less than 1.5 ml, change to buffer and proceed with the
injection until a total of 1.5 ml has been eluted. Discard the eluted liquid.
6. Elute the protein with the appropriate volume selected from Table A1.7 and collect the
desalted protein.
Note: 5 ml/min corresponds to approximately 120 drops/min when using a HiTrap 5 ml
column. A simple peristaltic pump or a chromatography system can also be used
for the desalting procedure.
11000421 AC 135
The maximum recommended sample volume is 1.5 ml. See Table A1.7 for the effect of
reducing the sample volume applied to the column.
Table A1.7. Recommended sample and elution volumes using a syringe
Sample load
(ml)
Add buffer
(ml)
Elute and collect Yield

(ml)
(%)
Remaining salt
(%)
Dilution
factor
0.25
1.25
1.0
> 95
0.0
4.0
0.50
1.0
1.5
> 95
< 0.1
3.0
1.00
0.5
2.0
> 95
< 0.2
2.0
1.50
2.0
> 95
< 0.2
1.3
Removal of lipoproteins
Lipoproteins and other lipid material can rapidly clog chromatography columns and it is advisable
to remove them before beginning purification. Precipitation agents such as dextran sulfate and
polyvinylpyrrolidine, described under Fractional precipitation above, are recommended to remove
high levels of lipoproteins from samples such as ascitic fluid.
Centrifuge samples when performing precipitation to avoid the risk of nonspecific binding
of the target molecule to a filter.
Samples such as serum can be filtered through glass wool to remove remaining lipids.
Removal of phenol red

Phenol red is frequently used at laboratory scale as a pH indicator in cell culture. Although not
directly interfering with purification, phenol red binds to certain purification media and should
be removed as early as possible to avoid the risk of contamination. It is known to bind to anion
exchange media at pH > 7.0.
Use a desalting column to simultaneously remove phenol red (a low molecular weight
molecule) and transfer sample to the correct buffer conditions for further purification,
as described under Buffer exchange and desalting earlier in this appendix.
Removal of low molecular weight contaminants

If samples contain a high level of low molecular weight contaminants, use a desalting
column before the first chromatographic purification step, as described under Buffer
exchange and desalting earlier in this appendix.
136 11000421 AC
Appendix 2
Nonvolatile and volatile buffer systems
Nonvolatile buffers for anion exchange chromatography
pH 4
10
pKa 1
(25C)
11
N-Methyl piperazine
Piperazine
4.75
5.33
bis-Tris
6.48
6.65; 9.1 0
bis-Trispropane
Triethhanolamine
Tris
N-Methyldiethanolamine
Propane-1,3-Diamino
7.76
8.07
8.52
8.88
9.50
9.73
Ethanolamine
Piperazine
Propane-1,3-Diamino
Piperidine
10.55
11.12
pH interval
Substance
Conc. (mM)
Counterion
4.3 to 5.3
N-Methylpiperazine
20
Cl
4.8 to 5.8
Piperazine
20
Cl or HCOO
5.5 to 6.5
L-Histidine
20
Cl-
6.04
6.0 to 7.0
bis-Tris
20
Cl-
6.48
6.2 to 7.2; 8.6 to 9.6 bis-Tris propane
20
Cl-
6.65; 9.10
7.3 to 8.3
Triethanolamine
20
Cl- or CH3COO - 7.76
-0.020
7.6 to 8.6
Tris
20
Cl-
8.07
-0.028
2-
pKa (25C)1
d(pKa)/dT (C)
4.75
-0.015
5.33
-0.015
-0.017
8.0 to 9.0
20
SO4
8.52
-0.028
8.0 to 9.0
50
Cl- or CH3COO - 8.52
-0.028
8.4 to 9.4
Diethanolamine
20 at pH 8.4 Cl
50 at pH 8.8
8.4 to 9.4
Propane 1,3-Diamino
9.0 to 10.0
8.88
-0.025
20
Cl-
8.88
-0.031
Ethanolamine
20
Cl-
9.50
-0.029
9.2 to 10.2
Piperazine
20
Cl
9.73
-0.026
10.0 to 11.0
Propane 1,3-Diamino
20
Cl-
10.55
-0.026
10.6 to 11.6
Piperidine
20
Cl
11.12
-0.031
Ref: Handbook of chemistry and physics, 83 edition, CRC, 2002 to 2003.

rd
11000421 AC 137
Nonvolatile buffers for cation exchange chromatography

pH 2.5
Citric acid
Lactic acid
Butanedioic acid (succinic acid)
Acetic acid
Methyl malonic acid
MES
Phosphate
HEPES
BICINE
pKa 1
(25C)
3.13
3.86
4.21
4.75
5.76
6.27
7.20
7.56
8.33
pH interval
Substance
Conc. (mM)
Counterion
pKa (25C)1
1.4 to 2.4
Maleic acid
20
Na
1.92
2.6 to 3.6
Methyl malonic acid
20
Na or Li
2.6 to 3.6
Citric acid
20
Na+
3.13
3.3 to 4.3
Lactic acid
50
Na
3.86
3.3 to 4.3
Formic acid
50
Na+ or Li+
3.75
+0.0002
3.7 to 4.7; 5.1 to 6.1
Succinic acid
50
Na
4.21; 5.64
-0.0018
4.3 to 5.3
Acetic acid
50
Na+ or Li+
4.75
+0.0002
5.2 to 6.2
Methyl malonic acid
50
Na or Li
5.76
5.6 to 6.6
MES
50
Na+ or Li+
6.27
-0.0110
6.7 to 7.7
Phosphate
50
Na
7.20
-0.0028
7.0 to 8.0
HEPES
50
Na+ or Li+
7.56
-0.0140
7.8 to 8.8
BICINE
50
Na
8.33
-0.0180
+
+
d(pKa)/dT (C)
3.07
-0.0024
Ref: Handbook of chemistry and physics, 83rd edition, CRC, 2002 to 2003.
Volatile buffer systems

pH range
Buffer system
Counterion
pKa-values for buffering ions1
3.3 to 4.3
Formic acid
3.75
3.3 to 4.3; 4.8 to 5.8
Pyridine/formic acid
HCOO
3.3 to 4.3; 9.3 to 10.3 Trimethylamine/formic acid
HCOO -
4.3 to 5.8
CH3COO
Pyridine/acetic acid
3.75; 5.25
4.75; 9.81
-
4.75; 5.25
4.3 to 5.3; 9.3 to 10.3 Trimethylamine/acetic acid
CH3COO -
4.75; 9.81
3.3 to 4.3; 8.8 to 9.8
Ammonia/formic acid
HCOO
3.75; 9.25
4.3 to 5.3; 8.8 to 9.8
Ammonia/acetic acid
CH3COO -
23
4.75; 9.25
5.9 to 6.9; 9.3 to 10.3 Trimethylamine/carbonate
CO
6.35; 9.81
5.9 to 6.9; 8.8 to 9.8
HCO3-
6.35; 9.25
Ammonium bicarbonate
23
5.9 to 6.9; 8.8 to 9.8
Ammonium carbonate/ammonia
CO
5.9 to 6.9; 8.8 to 9.8
Ammonium carbonate
CO32-
4.3 to 5.3: 7.2 to 8.2
N-Ethylmorpholine/acetate
HCOO
6.35; 9.25
6.35; 9.25
-
Ref: Handbook of chemistry and physics, 83rd edition, CRC, 2002 to 2003.
138 11000421 AC
4.75; 7.72
Appendix 3
Column packing and preparation
Prepacked columns from GE will ensure reproducible results and the highest performance.
Use small prepacked columns for media scouting and method optimization, to increase
efficiency in method development, for example, HiTrap IEX Selection Kit.
Efficient column packing is essential for IEX separation, especially when using gradient elution.
A poorly packed column gives rise to poor and uneven flow, band broadening, and loss of
resolution. If column packing is required, the following guidelines will apply at all scales of
operation:
With a high binding capacity medium, use short, wide columns (typically 5 to 15 cm bed
height) for rapid purification, even at low flow velocity.
The amount of IEX medium required will depend on the binding capacity of the medium and
the amount of sample. Binding capacities for each medium are given in this handbook and
supplied with the product instructions. Estimate the amount of medium required to bind
the sample of interest and use five times this amount to pack the column. The amount of
medium required can be reduced if resolution is satisfactory.
Once separation parameters have been determined, scale up a purification by increasing
the diameter of the column to increase column volume. Avoid increasing the length of the
column, if possible, as this will alter separation conditions.
IEX media can be packed in either Tricorn, XK, or HiScale columns available from GE. A step-bystep demonstration of column packing can be seen in Column Packing The Movie (Fig A3.1),
available in CD format (see Ordering information).
Fig A3.1. Column Packing The Movie provides a step-by-step demonstration of column packing.
11000421 AC 139
1. Equilibrate all materials to the temperature at which the separation will be performed.
2. Eliminate air by flushing column end pieces with the recommended buffer. Ensure no
air is trapped under the column net. Close column outlet leaving 1 to 2 cm of buffer in
the column.
3. Gently resuspend the medium.
Note that IEX media from GE are supplied ready to use. Decanting of fines that could clog the
column is unnecessary.
Avoid using magnetic stirrers since they can damage the matrix.
4. Estimate the amount of slurry (resuspended medium) required on the basis of the
recommendations supplied.
5. Pour the required volume of slurry into the column. Pouring down a glass rod held
against the wall of the column will minimize the introduction of air bubbles.
6. Immediately fill the column with buffer.
7. Mount the column top piece and connect to a pump.
8. Open the column outlet and set the pump to the desired flow rate.
When slurry volume is greater than the total volume of the column, connect a second
glass column to act as a reservoir (see Ordering information for details). This ensures
that the slurry has a constant diameter during packing, minimizing turbulence and
improving column packing conditions.
If the recommended flow rate cannot be obtained, use the maximum flow rate the
pump can deliver.
Do not the
exceed
the maximum
operating
medium
orheight
column.
9. Maintain
packing
flow rate for
at least pressure
3 CV afterofathe
constant
bed
is obtained.
Mark the bed height on the column.
Do not exceed 75% of the packing flow rate during any purification.
10. Stop the pump and close the column outlet. Remove the top piece and carefully fill
the rest of the column with buffer to form an upward meniscus at the top.
11. Insert the adapter into the column at an angle, ensuring that no air is trapped
under the net.
12. Slide the adapter slowly down the column (the outlet of the adaptor should be open)
until the mark is reached. Lock the adapter in position.
13. Connect the column to the pump and begin equilibration. Reposition the adapter
if necessary.
The medium must be thoroughly washed to remove the storage solution, usually 20%
ethanol. Residual ethanol can interfere with subsequent procedures.
Many media equilibrated with sterile phosphate-buffered saline containing an
antimicrobial agent may be stored at 4C for up to 1 mo, but always follow the specific
storage instructions supplied with the product.
140 11000421 AC
Column selection
Tricorn, XK, and HiScale columns are fully compatible with the high flow rates achievable with
modern media and a broad range of column dimensions are available. Columns most suitable
for packing IEX media are listed under the column packing section for each IEX medium
(Chapter 3). In most cases the capacity of the IEX medium and the amount of sample to be
purified will determine the column size required.
Column packing and efficiency

Column efficiency is expressed as the number of theoretical plates per meter chromatography bed
(N) or as H (height equivalent to a theoretical plate, HETP), which is the bed length (L) divided
by the plate number. Column efficiency is related to the band broadening that can occur on a
column and can be calculated from the expression:
N = 5.54
( )
VR
Wh
VR = volume eluted from the start of sample application to the peak maximum
wh = peak width measured as the width of the recorded peak at half of the peak height
H is calculated from the expression:
H=
L
N
L = height of packed bed.

Measurements of VR and wh can be made in distance (mm) or volume (ml) but both
parameters must be expressed in the same unit.
Column performance should be checked at regular intervals by injecting acetone to determine
column efficiency (N) and peak symmetry (asymmetry factor, As). Since the observed value for
N depends on experimental factors such as flow rate and sample loading, comparisons must
be made under identical conditions. In IEX, efficiency is measured under isocratic conditions by
injecting acetone (which does not interact with the medium) and measuring the eluted peak as
shown in Figure A3.2.
Absorbance
Ve
wh
50%
10%
Volume
Fig A3.2. Measurements taken to calculate column efficiency.
As a general rule, a good H value is about two to three times the average particle diameter of
the medium being packed. For a 90 m particle, this means an H value of 0.018 to 0.027 cm.
11000421 AC 141
The asymmetry factor (As) is expressed as:

As =
b
a
where
a = First half peak width at 10% of peak height
b = Second half peak width at 10% of peak height
As should be as close as possible to 1.0. A reasonable As value for a short column as used in
IEX is 0.80 to 1.80.
An extensive leading edge is usually a sign that the medium is packed too tightly and
extensive tailing is usually a sign that the medium is packed too loosely.
Run at least two column volumes of buffer through a newly packed column to ensure
that the medium is equilibrated with start buffer. Use pH monitoring to check the pH
of the eluent.
142 11000421 AC
Appendix 4
Selection of purification equipment
Simple IEX, such as elution by a step-gradient, can be performed using a syringe or
peristaltic pump with prepacked HiTrap columns. A chromatography system is required
when reproducible results are important and when manual purification becomes too timeconsuming and inefficient. This can be the case when large sample volumes are handled, or
when there are many different samples to be purified. The progress of the purification can be
monitored automatically and high-resolution separations with accurately controlled lineargradient elution can be performed.
Table A4.1 lists the standard KTA system configurations for currently available systems, see
also KTA Laboratory-scale Systems: Instrument Management Handbook, 29010831. Table 4.2
on the next page provides a summary of prepacked IEX columns for use with KTA systems.
Table A4.1. Ways of working with standard KTA chromatography systems
Automated and reproducible

protein purification using all
common techniques including
support for gradient elution
KTA start
KTAprime plus
KTAxpress
KTA pure
KTA avant
Software compatible with

regulatory requirements, e.g.,
good laboratory practice (GLP)
Method development and
optimization using design
of experiments (DoE)
Automatic buffer preparation

including pH scouting
Process development 4
Simple, one-step desalting,

buffer exchange
Research 4
Way of working
Automatic medium or column

scouting
Automatic, multistep purification
Scale-up, process development
0.1 to 50.0
0.1 to 65.0
0.001 to 25.0
(KTA pure 25)/
0.01 to 150
(KTA pure 150)
0.001 to 25/0.01
to 150
Flow rate (ml/min)
Max. operating pressure (MPa)

Software1 for system control
and data handling
0.5 to 5.0
0.5
20/5
20/5
UNICORN
start
PrimeView2
UNICORN 5
UNICORN 6
or later
UNICORN 6
or later
A specific software version might be needed for the chosen system. See the web page for each respective system at
www.gelifesciences.com/AKTA.
With PrimeView, you can monitor results and evaluate data but not create methods nor control the system.
= included
o = optional
11000421 AC 143
Table A4.2. Summary of prepacked columns for IEX using KTA systems
Chromatography
technique
Base matrix
Ion exchange
HiScreen
HiPrep
Easy to use
with a syringe,
peristaltic
pump, or
chromatography
system
Optimized
for method
and process
development
Convenient
Fast with good High quality and Microscale-up
resolution
high resolution purification
Preparative
and analysis
size exclusion
chromatography
Sepharose HP,
Sepharose FF
Capto,
Capto ImpRes
Capto ImpAct
RESOURCE
Tricorn (GL/PE)
MonoBeads
MiniBeads
SOURCE
System
compatibility
1
2
3
4
5
6
7
KTA pure
KTA start
KTAxpress
KTAprime plus
KTApurifier2
KTAexplorer3
KTAFPLC4
KTA avant
KTA pure 150
KTApurifier 1002
KTAexplorer 1003
KTA pure
KTA start5
KTA avant
KTAxpress
KTAprime plus
KTApurifier2
KTAexplorer3
KTAFPLC4
KTA pure
KTAmicro6
KTApurifier 102
KTAexplorer 103
KTAFPLC4
KTA pure 25
KTAmicro6
KTAxpress
KTAmicro6
KTApurifier 102
KTAexplorer 103
KTAFPLC4
Sample volume.
KTApurifier has been discontinued and replaced by KTA pure.
KTAexplorer has been discontinued and replaced by KTA avant.
KTAFPLC has been discontinued and replaced by KTA pure 25.
HiPrep 26/60 can be used but is not optimal.
KTAmicro has been discontinued and replaced by KTA pure 25 with microgram-scale purification flow path.
Precision Columns (PC) provide excellent results when used in combination with HPLC systems.
144 11000421 AC
Precision
Columns (PC)7
HiTrap
Appendix 5
Converting from flow velocity to
volumetric flow rates
It is convenient when comparing results for columns of different sizes to express flow as flow
velocity (cm/h). However, flow is usually measured in volumetric flow rate (ml/min). To convert
between flow velocity and volumetric flow rate use one of the formulae below.
From flow velocity (cm/h) to volumetric flow rate (ml/min)

Volumetric flow rate (ml/min) =

60
column cross sectional area (cm2)
p d
60
where
Y = flow velocity in cm/h
d = column inner diameter in cm
Example:
What is the volumetric flow rate in an XK 16/70 column (i.d. 1.6 cm) when the flow velocity
is 150 cm/h?
Y = flow velocity = 150 cm/h
d = inner diameter of the column = 1.6 cm
Volumetric flow rate =
150 p 1.6 1.6

60 4
ml/min
= 5.03 ml/min
From volumetric flow rate (ml/min) to flow velocity (cm/h)

Flow velocity (cm/h) =
Volumetric flow rate (ml/min) 60

column cross sectional area (cm2)
= Z 60
pd
where
Z = volumetric flow rate in ml/min
d = column inner diameter in cm
Example:
What is the linear flow in a Tricorn 5/50 column (i.d. 0.5 cm) when the volumetric flow rate is 1 ml/min?
Z = volumetric flow rate = 1 ml/min
d = column inner diameter = 0.5 cm
Flow velocity = 1 60
p 0.5 0.5
cm/h
11000421 AC 145
From volumetric flow rate (ml/min) to using a syringe

1 ml/min = approximately 30 drops/min on a HiTrap 1 ml column
5 ml/min = approximately 120 drops/min on a HiTrap 5 ml column
146 11000421 AC
Appendix 6
Conversion data: proteins, column pressures
Proteins
Mass (g/mol) 1 g
1 nmol
Protein
A280 for 1 mg/ml
10 000
100 pmol; 6 10 molecules
10 g
IgG
1.35
50 000
20 pmol; 1.2 1013 molecules
50 g
IgM
1.20
100 000
10 pmol; 6.0 1012 molecules
100 g
IgA
1.30
150 000
6.7 pmol; 4.0 1012 molecules
150 g
Protein A
0.17
Avidin
1.50
Streptavidin
3.40
Bovine serum albumin
0.70
1 kb of DNA
13
= 333 amino acids of coding capacity

= 37 000 g/mol
270 bp DNA
= 10 000 g/mol
1.35 kb DNA
= 50 000 g/mol
2.70 kb DNA
= 100 000 g/mol
Average molecular weight of an amino acid = 120 g/mol.
Column pressures
The maximum pressure drop over the packed bed refers to the pressure above which the column
contents might begin to compress.
Pressure units may be expressed in megaPascal (MPa), bar, or pounds per square inch (psi) and
can be converted as follows: 1 MPa = 10 bar = 145 psi
11000421 AC 147
Appendix 7
Table of amino acids
Amino acid
Three-letter
code
Single-letter
code
Ala
Structure
HOOC
Alanine
CH3
H2N
NH2
HOOC
Arginine
Arg
CH2CH2CH2NHC
H2N
NH
HOOC
Asparagine
Asn
Aspartic acid
Asp
Cysteine
Cys
Glutamic acid
Glu
Glutamine
Gln
Glycine
Gly
Histidine
His
CH2CONH2
H2N
HOOC
CH2COOH
H2N
HOOC
CH2SH
H2N
HOOC
CH2CH2COOH
H2N
HOOC
CH2CH2CONH2
H2N
HOOC
H
H2N
HOOC
N
CH2
NH
H2N
HOOC
Isoleucine
Ile
Leucine
Leu
CH(CH3)CH2CH3
H2N
HOOC
CH3
CH2CH
CH3
H2N
HOOC
Lysine
Lys
Methionine
Met
Phenylalanine
Phe
Proline
Pro
CH2CH2CH2CH2NH2
H2N
HOOC
CH2CH2SCH3
H2N
HOOC
CH2
H2N
HOOC
H2N
NH
HOOC
Serine
Ser
Threonine
Thr
CH2OH
H2N
HOOC
CHCH3
H2N
OH
HOOC
Tryptophan
Trp
CH2
H2N
NH
HOOC
Tyrosine
Tyr
Valine
Val
CH2
H2N
HOOC
148 11000421 AC
CH(CH3)2
H2N
OH
Middle unit
residue (-H20)
Formula
Mr
Charge at
Hydrophobic
pH 6.0 to 7.0
(nonpolar)
Uncharged
(polar)
Formula
Mr
C3H7NO2
89.1
C3H5NO
71.1
Neutral
C6H14N4O2
174.2
C6H12N4O
156.2
Basic (+ve)
C4H8N2O3
132.1
C4H6N2O2
114.1
Neutral
C4H7NO4
133.1
C4H5NO3
115.1
Acidic(-ve)
C3H7NO2S
121.2
C3H5NOS
103.2
Neutral
C5H9NO4
147.1
C5H7NO3
129.1
Acidic (-ve)
C5H10N2O3
146.1
C5H8N2O2
128.1
Neutral
C2H5NO2
75.1
C2H3NO
57.1
Neutral
C6H9N3O2
155.2
C6H7N3O
137.2
Basic (+ve)
C6H13NO2
131.2
C6H11NO
113.2
Neutral
C6H13NO2
131.2
C6H11NO
113.2
Neutral
C6H14N2O2
146.2
C6H12N2O
128.2
Basic (+ve)
C5H11NO2S
149.2
C5H9NOS
131.2
Neutral
C9H11NO2
165.2
C9H9NO
147.2
Neutral
C5H9NO2
115.1
C5H7NO
97.1
Neutral
C3H7NO3
105.1
C3H5NO2
87.1
Neutral
C4H9NO3
119.1
C4H7NO2
101.1
Neutral
C11H12N2O2
204.2
C11H10N2O
186.2
Neutral
C9H11NO3
181.2
C9H9NO2
163.2
Neutral
C5H11NO2
117.1
C5H9NO
99.1
Neutral
Hydrophilic
(polar)
11000421 AC 149
Appendix 8
Analytical assays during purification
Analytical assays are essential to follow the progress of purification. They are used to assess the
effectiveness of each step in terms of yield, biological activity, and recovery as well as to help
during optimization of experimental conditions. The importance of a reliable assay for the
target molecule cannot be overemphasized.
When testing chromatographic fractions, ensure that the buffers used for purification
do not interfere with the assay.
Total protein determination

Lowry or Bradford assays are used most frequently to determine the total protein content. The
Bradford assay is particularly suited to samples where there is a high lipid content that can
interfere with the Lowry assay.
Purity determination
Purity is most often estimated by SDS-PAGE. Alternatively, isoelectric focusing, capillary
electrophoresis, reversed phase chromatography, or mass spectrometry may be used.
SDS-PAGE analysis
The general steps involved in SDS-PAGE analysis are summarized below.
1. Prepare samples by mixing with equal volume of 2x SDS loading buffer
2. Vortex briefly and heat for 5 min at 90C to 100C.
3. Load the samples and, optionally, a MW marker onto a SDS-polyacrylamide gel.
4. Run the gel.
5. Stain the gel with Coomassie Blue (Coomassie Blue Tablets, PhastGel Blue R-350) or
silver (PlusOne Silver Staining Kit, Protein).
The percentage of acrylamide in the SDS gel should be selected according to the
expected molecular weight of the protein of interest (see Table A8.1).
Table A8.1. Percentage of acrylamide used in SDS gels for proteins of different molecular weights
Acrylamide in resolving gel (%)
Mol. weight range
Homogeneous:
36 000 to 200 000
7.5
24 000 to 200 000
10
14 000 to 200 000
12.5
14 000 to 100 000
15
14 000 to 60 0001
5 to 15
14 000 to 200 000
5 to 20
10 000 to 200 000
10 to 20
10 000 to 150 000
Gradient:
The larger proteins fail to move significantly into the gel.
150 11000421 AC
The gel is usually stained after electrophoresis in order to make the protein bands visible by, for
example, Coomassie Blue or silver staining. A more recent way of making protein visible is by
prelabeling the proteins by fluorescent dye (Amersham WB Cy5 dye reagent) before loading
the sample in the gel. By doing in this way the gel image can be acquired directly after finished
electrophoresis by laser scanner or CCD camera and the result is obtained much faster. This
workflow is outlined below.
Protein prelabeling with CyDye

1. Prepare samples by prelabeling with Amersham WB Cy5 dye reagent.
2. Vortex briefly and heat for 5 min at 90C to 100C.
3. Load the samples and, optionally, a MW marker onto a SDS-polyacrylamide gel.
4. Run the gel and proceed directly to image capture.
For information and advice on electrophoresis techniques, refer to the handbook
2-D Electrophoresis, Principles and Methods, 80642960. For information on the
Amersham WB system and accessories including Amersham WB Cy5 prelabeling
reagents, visit www.gelifesciences.com/westernblotting.
Functional assays
Immunospecific interactions have enabled the development of many alternative assay systems
for the assessment of active concentration of target molecules.
Western blot analysis is used to confirm protein identity and quantitate the level of
target molecule.
1. Separate the protein samples by SDS-PAGE.
2. Transfer the separated proteins from the gel to an appropriate membrane, depending
on the choice of detection reagents. Amersham Protran (NC) or Amersham Hybond P
(PVDF) membranes are recommended for chemiluminescent detection using
Amersham ECL start, Amersham ECL, Amersham ECL Prime, or Amersham ECL Select
Western blotting detection reagents. Amersham Protran Premium (NC) or
Amersham Hybond LFP (PVDF) membranes are recommended for fluorescent detection
with Amersham ECL Plex Western blotting detection system.
3. Develop the membrane with the appropriate specified reagents.
Electrophoresis, protein transfer, and probing may be accomplished using a variety
of equipment and reagents. The Amersham WB system is an automated system that
can be used for all these steps including software evaluation. For more information,
visit www.gelifesciences.com/westernblotting. For further on the basic principles and
methods used in Western blotting, refer to the Western Blotting Handbook, 28999897
and the instruction manuals supplied with the detection kits.
ELISAs are most commonly used as activity assays.
Functional assays using the phenomenon of surface plasmon resonance (SPR) to detect
immunospecific interactions (e.g., using Biacore systems) enable the determination of
active concentration, epitope mapping, and studies of interaction kinetics.
The Biacore Assay Handbook, 29019400 gives a general overview of the different types
of SPR-based applications. The handbook also provides advice on sample preparation,
design, and optimization of different assays.
11000421 AC 151
Detection and assay of tagged proteins

SDS-PAGE, Western blotting, and ELISA can also be applied to the detection and assay of
genetically engineered molecules to which a specific tag has been attached. In some cases,
an assay based on the properties associated with the tag itself can be developed, for example,
the GST Detection Module for enzymatic detection and quantitation of GST-tagged proteins.
Further details on the detection and quantitation of GST and (his)6-tagged proteins are available
in the Recombinant Protein Purification Handbook, 18114275 and the GST Gene Fusion System
Handbook, 18115758 from GE.
152 11000421 AC
Appendix 9
Storage of biological samples
The advice given here is of a general nature and cannot be applied to every biological
sample. Always consider the properties of the specific sample and its intended use
before following any of these recommendations.
General recommendations
Add stabilizing agents, when necessary. Stabilizing agents are often required for storage of
purified proteins.
Serum, culture supernatants, and ascitic fluid should be kept frozen at -20C or -70C, in
small aliquots.
Avoid repeated freeze/thawing or freeze drying/redissolving that can reduce biological activity.
Avoid conditions close to stability limits for example pH or salt concentrations, reducing or
chelating agents.
Keep refrigerated at 4C in a closed vessel to minimize bacterial growth and protease
activity. Above 24 h at 4C, add a preserving agent if possible (e.g., merthiolate 0.01%).
Sodium azide can interfere with many coupling methods and some biological
assays and can be a health hazard. It can be removed by using a desalting column
(see Appendix 1, Sample preparation).
Specific recommendations for purified proteins

Store as a precipitate in high concentration of ammonium sulfate, for example 4.0 M.
Freeze in 50% glycerol, especially suitable for enzymes.
Avoid the use of preserving agents if the product is to be used for a biological assay.
Preserving agents should not be added if in vivo experiments are to be performed.
Store samples in small aliquots and keep frozen.
Sterile filter to prolong storage time.
Add stabilizing agents such as glycerol (5% to 20%) or serum albumin (10 mg/ml) to help
maintain biological activity. Remember that any additive will reduce the purity of the protein
and might need to be removed at a later stage.
Avoid repeated freeze/thawing or freeze drying/redissolving that can reduce biological activity.
Certain proteins, including some mouse antibodies of the IgG3 subclass, should not be
stored at 4C as they precipitate at this temperature. Keep at room temperature in the
presence of a preserving agent.
11000421 AC 153
Appendix 10
Column cleaning
Correct preparation of samples and buffers and application of a high salt wash (1 M NaCl)
at the end of each separation should keep most columns in good condition. However, reduced
indications that the medium needs to be cleaned using more stringent procedures in order
to remove contaminants.
packing and interfere with performance. The cleaning procedure to remove common
contaminants is included with each of the media described in in Chapter 3.
Removing precipitated proteins, lipids, hydrophobically bound proteins,

or lipoproteins
To remove precipitated proteins
Use the recommended flow rate for cleaning of the media and column, see Chapter 3. When
guanidine hydrochloride is used, the flow rate should be lowered to half of this flow rate to
avoid overpressure.
1. Wash with 2 CV of 6 M guanidine hydrochloride.
2. Wash immediately with at least 5 CV of buffer at pH 7.0 to 8.0.
3. Rinse with at least 2 CV of distilled water until the UV-baseline and eluent pH are stable.
4. Wash with at least 4 CV of start buffer or storage buffer until pH and conductivity
values have reached the required values.
Alternatively,
1. Inject 1 CV of pepsin (1 mg/ml in 500 mM NaCl, 100 mM acetic acid). Leave overnight at
room temperature or for 1 h at 37C.
3. Wash with at least 4 CV of start buffer or storage buffer, until eluent pH and
To remove lipids, hydrophobically bound proteins, or lipoproteins

Organic solvents or detergents might be required to completely remove contaminants of this type.
Before using organic solvents, wash the medium with at least 4 CV of distilled water to
avoid salts precipitating on the column.
When applying organic solvents or solutions it might be necessary to reduce the flow
rate considerably to avoid overpressuring the column.
154 11000421 AC
Use cleaning solutions such as up to 30% isopropanol, up to 100% methanol, up to 100%

acetonitrile, up to 2 M NaOH, up to 75% acetic acid, up to 100% ethanol, ionic or nonionic detergents.
When cleaning larger columns, allow a contact time of 1 to 2 h for any solution that
is used as an initial cleaning step.
Always check for solvent compatibility in the instructions supplied with the medium
or column.
Avoid anionic detergents with Q, DEAE, and ANX charged groups. Avoid cationic detergents
with S, SP, and CM charged groups.
Extended cleaning procedures

Use the recommended flow rate and cleaning procedure for the media and column, see
Chapter 3. If this is not sufficient, extended cleaning procedures can be tested. When organic
solvents, such as 30% isopropanol or 70% ethanol are used, the flow rate should be lowered to
half of this flow rate to avoid overpressure.
1. Wash with 4 CV of up to 70% ethanol or 30% isopropanol.
2. Rinse with at least 2 CV of distilled water until the UV-baseline and eluent pH are stable.
3. Wash immediately with 3 CV of start buffer.
Alternatively,
1. Wash with 2 CV of detergent in a basic or acidic solution, for example, 0.1% to 0.5%
nonionic detergent in 100 mM acetic acid.
2. Rinse with 5 CV 70% ethanol to remove residual detergent.
3. Rinse with at least 2 CV of distilled water until the UV-baseline and the eluent pH
are stable.
11000421 AC 155
Appendix 11
Media selection
Using prepacked small columns such as HiTrap during the early stages of development saves
time, solvents and sample. HiTrap IEX Selection Kit allows quick and efficient screening for the
most suitable charge group and enables development of the basic method. The following are
descriptions of different screening methods for selection of media and optimal conditions.
Selection of media for automated purification

Users of KTA systems with automatic buffer preparation functionality can select from a range
of buffer recipes to test different media over a range of pH values and other elution conditions.
See KTA Laboratory-scale Chromatography Systems: Instrument Management Handbook,
29010831 for details of how to vary flow rate and gradient slope in order to optimize the separation.
Note that the condition of the sample is very important in order to achieve the most
effective separations. Samples should preferably have the same conditions as the start
buffer (see Buffer exchange and desalting in Appendix 1 for details). When working with
small volumes during screening and scouting, it might be sufficient to dilute the sample
in start buffer in order to lower the ionic strength and adjust the pH to a value similar to
that of the start buffer.
1. Scout for optimum pH by testing a range of pH values within which the proteins of
interest are known to be stable. If the pI of the target protein is known, then begin with
a narrower pH range, for example, 0.5 to 1.0 pH unit away from the pI. Typical results
from an automatic pH scouting run are shown in Figure A11.1.
2. If required, scout for optimum selectivity (testing strong or weak exchangers) using
automatic media scouting.
3. Scout for the steepest gradient that gives acceptable resolution at the selected pH.
4. Scout for the highest flow rate that maintains resolution and minimizes separation
time. Check recommended flow rates for the specific medium.
5. Scout for the maximum sample load that can be applied while maintaining satisfactory
resolution. In general, loading 20% to 30% of the total binding capacity of the column
gives optimal resolution with gradient elution.
Reduce separation time and buffer consumption by transfering to a step elution when
optimized separation conditions have been established. Sample loads can often be
increased when using a step elution.
156 11000421 AC
START CONDITIONS
pH
Run 1
Run 2
R un 3
Run 4
Run 5
Run 6
Run 7
6.5
5. 5
4. 5
80.0
250
A 280 nm
60.0
pH 4.0
150
pH 4.5
pH 5.0
100
40.0
pH 5.5
200
pH 6.0
50
pH 6.5
20.0
pH 7.0
0
2.0
4.0
6.0
8.0
Ti me (min)
Column:
Sample:
Eluents:
RESOURCE S, 6 ml
Fab fraction from HIC separation, 20 ml
Automatic BufferPrep with
60 mM sodium acetate,
30 mM sodium phosphate,
30 mM sodium formate
100 mM HCI and 2 M NaCI
Gradient: 20 column volumes, to 1 M NaCI
Flow rate: 60 ml/min
Curves:
A280nm, from top:
pH 4.0; 4.5; 5.0; 5.5; 6.0; 6.5; 7.0
Fig A11.1. Automatic pH scouting on an KTA system.
Selection of media for manual purification

HiTrap columns are well-suited to manual media screening, method development, and method
optimization since they can be used with a syringe or peristaltic pump as well as an automated
chromatography system.
Note that the condition of the sample is very important to achieve the most effective
separations. Samples should preferably have the same conditions the start buffer (see
Appendix 1, Sample preparation for details). When working with small volumes during
screening it might be sufficient to dilute the sample in start buffer in order to lower the
ionic strength and adjust the pH to a value similar to that of the start buffer.
Scout for optimum pH by testing a range of pH values within which the proteins of interest
are known to be stable. If the pI of the target protein is known, then begin with a narrower
pH range, for example, 0.5 to 1.0 pH unit away from the pI. The methods here are
optimized for use with 1 ml HiTrap columns and should be adjusted if other column
volumes are used.
Screening for IEX medium and pH conditions

1. Start buffers: set up a series of buffers with pH values in the range 4.0 to 8.0 (SP, CM) or
5.0 to 9.0 (Q, DEAE, ANX) and with 0.5 to 1.0 pH unit intervals between each buffer. See
Appendix 2 for recommended buffers.
2. Elution buffers: set up a second series of buffers with the same pH values, but including
1 M NaCl.
3. Equilibrate the column (s) with 5 ml start buffer at 1 ml/min. Wash with 5 ml elution buffer.
4. Re-equilibrate with 5 to 10 ml start buffer.
5. Adjust the sample to the pH of the start buffer and apply a known amount of the
sample at 1 ml/min. Collect eluate.
6. Wash with at least 5 ml of start buffer or until no material appears in eluent. Collect eluate.
7. Elute bound material with elution buffer (3 to 5 ml is usually sufficient, but other volumes
might be required dependent on the exact experimental conditions). Collect eluate.
11000421 AC 157
7. Elute bound material with elution buffer (3 to 5 ml is usually sufficient, but other volumes
might be required dependent on the exact experimental conditions). Collect eluate.
8. Analyze all eluates (for example by an activity assay) and determine purity and the
amount bound to the column.
9. Perform steps 3 to 8 for the next buffer pH.
10. Select medium and pH: the most suitable pH should allow the protein(s) of interest to
bind, but should be as close to their point of release as possible.
Screening for ionic strength conditions

1. Using the selected medium, start buffer and pH from the previous protocol, set up
a series of elution buffers at the same pH, but vary the salt concentration from 0 to
500 mM with intervals of 50 to 100 mM salt between each buffer.
2. Repeat steps 3 to 8 from the previous protocol for each salt concentration.
3. Determine the maximum ionic strength which permits binding of the protein(s) of
interest and the minimum ionic strength required for complete elution.
Further optimization
1. If gradient making equipment is available, determine the steepest gradient that
gives acceptable resolution at the selected pH. Begin with a gradient of 10 CV over
an ionic strength range based on the maximum and minimum values determined
when screening. Alternatively, begin with a gradient of 0% to 50% elution buffer that
contains 1 M NaCl and a gradient volume of 10 to 20 CV.
2. Determine the highest flow rate that maintains resolution and minimizes separation
time. Check recommended flow rates for the specific medium.
3. Determine the maximum sample load that can be applied while maintaining
satisfactory resolution. In general, loading 20% to 30% of the total binding capacity of
the column gives optimal resolution with gradient elution. Sample loads can often be
increased if resolution is satisfactory or when using a step elution.
Using PD-10 columns for media selection and method development

If an assay is available to detect the target protein(s), PD-10 columns can be packed with
various media and used to find the most suitable separation conditions. With basic information
on the requirements for pH and ionic strength, a suitable column can be packed in order to
begin optimization.
Note that the condition of the sample is very important in order to achieve the most
effective separations. Samples should preferably have the same conditions as the
start buffer (see Appendix 1, Sample preparation for details). When working with small
volumes during screening and scouting, it might be sufficient to dilute the sample in
start buffer in order to lower the ionic strength and adjust the pH to a value similar to
that of the start buffer.
158 11000421 AC
pH selection
1. Set up a series of 10 PD-10 columns for each medium to be tested and thoroughly
resuspend the medium in its storage solution.
2. Pour medium slurry containing 5 ml medium into the PD-10 column, allowing the
medium to settle as the column fills. Do not allow the column to dry out.
3. Equilibrate each column to a different pH by washing (5 5 ml) with buffer (500 mM)
using buffers between pH 5.0 to 9.0 for anion exchangers or pH 4.0 to 8.0 for cation
exchangers and with 0.5 pH unit intervals between columns (see Appendix 2 for buffer
recommendations).
4. Equilibrate each column at a lower ionic strength: wash with 5 5 ml of buffer (20 to
50 mM) at the same pH.
5. Load a known constant amount of sample to each column while collecting the eluent.
8. Assay the eluent for the protein of interest. The most suitable medium and pH should
allow the protein to bind (protein is absent from the eluent), but should be as close to
the point of release as possible (the first pH at which the protein appears in the eluent).
Ionic strength selection

1. Set up a series of 10 PD-10 columns, each containing 5 ml of the chosen IEX medium.
2. Equilibrate the column by washing (5 5 ml) with buffer (500 mM) at the selected
starting pH.
3. Equilibrate the columns at different ionic strengths, but constant pH, ranging from
10 to 300 mM NaCl by washing (5 5 ml). Intervals of 50 mM NaCl are sufficient.
4. Apply sample while collecting the eluent.
5. Assay the eluent to determine the maximum ionic strength which permits binding of
the target protein and the minimum ionic strength required for complete elution. The
highest ionic strength which permits binding and the lowest ionic strength for elution
are used as start and elution buffers, respectively, during subsequent gradient elution.
11000421 AC 159
Related literature
Code number
Purification handbooks
18102229
18103746
Hydrophobic Interaction and Reversed Phase Chromatography
11001269
Multimodal Chromatography
29054808
Protein Sample Preparation
28988741
Purifying Challenging Proteins
28909531
Recombinant Protein Purification
18114275
Size Exclusion Chromatography
18102218
Strategies for Protein Purification
28983331
KTA Laboratory-scale Chromatography Systems
29010831
Protein analysis handbooks

Biacore Assay
29019400
Biacore Sensor Surface
BR100571
Western Blotting
28999897
Selection guides and multimedia

Ion exchange columns and media, Selection guide
18112731
Prepacked chromatography columns for KTA systems, Selection guide
28931778
Column Packing - The Movie, CD
18116533
160 11000421 AC
Ordering information
Ion exchange
Product
Quantity
Code number
MiniBeads
Prepacked columns
Mini Q PC 3.2/3
1 0.24 ml
17068601
Mini S PC 3.2/3
1 0.24 ml
17068701
Mini Q 4.6/50 PE
1 0.8 ml
17517701
Mini S 4.6/50 PE
1 0.8 ml
17517801
Mono Q 5/50 GL
1 1 ml
17516601
Mono Q 10/100 GL
1 8 ml
17516701
Mono Q 4.6/100 PE
1 1.7 ml
17517901
Mono Q HR 16/10
1 20 ml
17050601
Mono S 5/50 GL
1 1 ml
17516801
MonoBeads
Prepacked columns
Mono S 10/100 GL
1 8 ml
17516901
Mono S 4.6/100 PE
1 1.7 ml
17518001
Mono S HR 16/10
1 20 ml
17050701
SOURCE 15
Chromatography media packs
SOURCE 15Q
10 ml
17094720
SOURCE 15Q
50 ml
17094701
SOURCE 15Q
200 ml
17094705
SOURCE 15S
10 ml
17094410
SOURCE 15S
50 ml
17094401
SOURCE 15S
200 ml
17094405
1 1 ml
17117701
Prepacked columns
RESOURCE Q
RESOURCE Q
1 6 ml
17117901
1 1.7 ml
17518101
RESOURCE S
1 1 ml
17117801
RESOURCE S
1 6 ml
17118001
SOURCE 15S 4.6/100 PE
1 1.7 ml
17518201
11000421 AC 161
Product
Quantity
Code number
SOURCE 30
SOURCE 30Q
10 ml
17127510
SOURCE 30Q
50 ml
17127501
SOURCE 30Q
200 ml
17127505
SOURCE 30S
10 ml
17127320
SOURCE 30S
50 ml
17127301
SOURCE 30S
200 ml
17127302
75 ml
17108701
75 ml
17101401
HiTrap Q HP
1 1 ml
29051325
HiTrap Q HP
5 1 ml
17115301
HiTrap Q HP
5 5 ml
17115401
HiPrep Q HP 16/10
1 20 ml
29018182
HiTrap SP HP
1 1 ml
29051324
HiTrap SP HP
5 1 ml
17115101
HiTrap SP HP
5 5 ml
17115201
HiScreen SP HP
1 4.7 ml
28950515
HiPrep SP HP 16/10
1 20 ml
29018183
25 ml
17051010
300 ml
17051001
25 ml
17072910
300 ml
17072901
25 ml
17070910
500 ml
17070901
25 ml
17071910
Sepharose High Performance

Prepacked columns
Sepharose Fast Flow

500 ml
17071901
25 ml
17128710
500 ml
17128701
7 1 ml
17600233
HiTrap Q FF
5 1 ml
17505301
HiTrap Q FF
5 5 ml
17515601
HiPrep Q FF 16/10
1 20 ml
28936543
Prepacked columns
HiTrap IEX Selection Kit
Kit contains seven HiTrap columns prepacked with Fast Flow (FF) media:
Q Sepharose FF, DEAE Sepharose FF, SP Sepharose FF, CM Sepharose FF,
ANX Sepharose FF(high sub), Q Sepharose XL, and SP Sepharose XL
162 11000421 AC
Product
Quantity
HiTrap SP FF
5 1 ml
Code number
17505401
HiTrap SP FF
5 5 ml
17515701
HiPrep SP FF 16/10
1 20 ml
28936544
HiTrap DEAE FF
5 1 ml
17505501
HiTrap DEAE FF
5 5 ml
17515401
HiPrep DEAE FF 16/10
1 20 ml
28936544
HiTrap CM FF
5 1 ml
17505601
HiTrap CM FF
5 5 ml
17515501
HiPrep CM FF 16/10
1 20 ml
28936542
HiTrap ANX FF (high sub)
5 1 ml
17516201
5 5 ml
17516301
Sepharose XL
Q Sepharose XL
300 ml
17507201
SP Sepharose XL
300 ml
17507301
HiTrap Q XL
5 1 ml
17515801
HiTrap Q XL
5 5 ml
17515901
HiPrep Q XL 16/10
1 20 ml
28936538
HiTrap SP XL
5 1 ml
17516001
HiTrap SP XL
5 5 ml
17516101
HiPrep SP XL 16/10
1 20 ml
28936540
1l
17098903
1l
17065703
25 ml
17531610
Prepacked columns
Sepharose Big Beads

Capto
Capto Q
Capto Q
100 ml
17531602
Capto S
25 ml
17544110
Capto S
100 ml
17544101
Capto DEAE
25 ml
17544310
Capto DEAE
100 ml
17544301
5 1 ml
28934388
Prepacked columns
HiTrap Capto IEX Selection Kit
Contains five HiTrap columns prepacked with: Capto Q, Capto S,
Capto DEAE, Capto MMC, Capto adhere
HiTrap Capto Q
5 1 ml
11001302
HiTrap Capto Q
5 5 ml
11001303
HiScreen Capto Q
1 4.7 ml
28926978
11000421 AC 163
Product
Quantity
HiTrap Capto S
5 1 ml
Code number
17544122
HiTrap Capto S
5 5 ml
17544123
HiScreen Capto S
1 4.7 ml
28926979
HiTrap Capto DEAE
5 1 ml
28916537
HiTrap Capto DEAE
5 5 ml
28916540
HiScreen Capto DEAE
1 4.7 ml
28926982
25 ml
17547010
Capto ImpRes
Capto Q ImpRes
Capto Q ImpRes
100 ml
17547002
Capto SP ImpRes
25 ml
17546810
Capto SP ImpRes
100 ml
17546802
Prepacked columns
HiTrap Capto Q ImpRes
5 1 ml
17547051
5 5 ml
17547055
HiScreen Capto Q ImpRes
1 4.7 ml
17547015
HiTrap Capto SP ImpRes
5 1 ml
17546851
5 5 ml
17546855
HiScreen Capto SP ImpRes
4.7 ml
17546815
Capto S ImpAct
25 ml
17371701
Capto S ImpAct
100 ml
17371702
Capto ImpAct
Prepacked columns
HiTrap Capto S ImpAct
5 1 ml
17371751
5 5 ml
17371755
HiScreen Capto S ImpAct
1 4.7 ml
17371747
SOURCE, Sepharose High Performance, Sepharose Fast Flow, Sepharose XL,

Sepharose Big Beads, and Capto are all available as BioProcess media for
large-scale production. Visit www.gelifesciences.com/bioprocess
Prepacked desalting columns

HiTrap Desalting
1 5 ml
29048684
HiTrap Desalting
5 5 ml
17140801
1 53 ml
17508701
4 53 ml
17508702
PD-10 Desalting Column
30
17085101
164 11000421 AC
Product
Quantity
Code number
Empty columns
Tricorn 10/100
18116315
XK 16/20
18877301
XK 26/20
18100072
XK 50/20
18100071
Empty Disposable PD-10 Desalting columns
50/pk
17043501
LabMate PD-10 Buffer Reservoir
18321603
Packing Connector XK 16
18115344
Packing Connector XK 26
18115345
Packing equipment 10/100 (Tricorn)
18115325
Packing Connector 10-10
18115323
Acessories and spare parts
11000421 AC 165
Product index
A
KTA avant
143144
F
FineLINE 100 column
6970, 126
KTAexplorer
144
FineLINE 800 column
126
KTAFPLC
144
FineLine Pilot 35 column
126
KTAprime plus
143144
KTApurifier
144
KTA pure
53, 143
H
HiPrep CM FF 16/10
85, 163
KTA start
143144
HiPrep DEAE FF 16/10
86, 163
KTAxpress
143144
HiPrep Q FF 16/10
84, 87, 162
Amersham ECL
151
HiPrep Q XL 16/10
92, 116, 163
Amersham ECL Plex
151
HiPrep SP FF 16/10
84, 163
Amersham ECL Prime
151
HiPrep SP HP 16/10
7677, 162
Amersham ECL Select
151
Amersham Hybond LFP
151
Amersham Hybond P
151
Amersham Protran Premium
151
Amersham WB
(Western blotting) Cy5
151
Amersham WB system
151

(high sub)
24, 8284, 122, 162
HiPrep SP XL 16/10
92, 163
119, 135, 164
HiScreen Capto DEAE
104, 164
HiScreen Capto Q
104, 164
HiScreen Capto Q ImpRes
104, 123124
HiScreen Capto S
104, 164
HiScreen Capto S ImpAct
104, 125, 164
HiScreen Capto SP ImpRes
104, 164
82, 84, 163
HiTrap Capto DEAE
104, 164
HiTrap Capto Q
104, 164
104, 164
HiTrap Capto S
104, 164
104, 164
104, 164
HiTrap CM FF
8586, 93
HiTrap DEAE FF
82, 84, 163
102104, 110, 122,

123
HiTrap Desalting
131, 135, 164
Capto Q
102104, 110, 118,

122, 123, 163
HiTrap Heparin HP
62
HiTrap IEX Selection Kit
Capto Q ImpRes
102104, 110,
122124, 164
30, 91, 116, 139,

156, 162
HiTrap Q FF
82, 84, 87, 162

41, 42, 76, 78, 162
Axichrom 1000 column
105
B
Benzamidine Sepharose 4 Fast
Flow (high sub)
51
BPG 300 column
98
BPG 450 column
105
C
Capto DEAE
Capto S
102106, 122123, 163
HiTrap Q HP
Capto S ImpAct
2829, 102104,
107108, 110, 118,
122, 125, 164
HiTrap Q XL
82, 9293, 163
HiTrap SP FF
84, 86, 93, 163
HiTrap SP HP
7678, 162
86, 9293, 163
Capto SP ImpRes
102104, 106107,
110, 122, 124, 164
HiTrap SP XL
24, 83, 85, 90, 122, 162
Column Packing - The Movie
139, 160
INdEX 70 column
D
166 11000421 AC
94
L
24, 8384, 122123,
162
LabMate PD-10 Buffer Reservoir
165
LMW-SDS Marker Kit
62
Mini Q 4.6/50 PE
5455, 161
Sephadex G-25
131, 133134
Mini Q PC 3.2/3
54, 56, 161
SOURCE 15Q
28, 62, 68
Mini S 4.6/50 PE
5455, 161
62, 68, 71, 161
Mini S PC 3.2/3
5455, 161
SOURCE 15S
6769, 122, 126, 161
Mono Q 10/100 GL
61, 161
SOURCE 15S 4.6/100 PE
68, 161
Mono Q 4.6/100 PE
61, 161
SOURCE 30Q
Mono Q 5/50 GL
34, 6163, 161
29, 35, 6768, 70,

122, 125, 162
Mono Q HR 16/10
61, 161
SOURCE 30S
Mono S 10/100 GL
61, 161
38, 6768, 71, 122,

125126, 162
Mono S 4.6/100 PE
61, 161
9899, 101, 122, 163
Mono S 5/50 GL
6163, 119, 161
23, 8384, 90
122123, 162
Mono S HR 16/10
61, 161
P
PD MiniTrap G-25
7576, 81, 102, 124,

162
135
SP Sepharose XL
91, 122123, 162163
PD-10 Desalting column
78, 164165
SPARTAN 13 mm HPLC-Certified
Syringe Filter, RC, 0.2 m
130
PhastGel Homogeneous 12.5
62
Syringe Filter, RC, 0.45 m
130
PhastSystem electrophoresis unit 62

PlusOne Coomassie Tablets,
PhastGel Blue R-350
150
Syringe Filter, RA, 0.2 m
130
PlusOne Silver Staining Kit, Protein 150
Syringe Filter, RA, 0.45 m
130
Superdex 75 prep grade
120
PrimeView software
143
Puradisc 4 Syringe Filter,

0.2 m, PVDF
130

0.2 m, PVDF
130

0.2 m, PVDF
130
Superdex 200 Increase 10/300 GL 108

T
Tricorn 10/100
68, 77, 85, 92, 165
Tricorn 10/150
68, 77, 85, 92
Tricorn 10/200
68, 77, 85, 92
Tricorn 5/100
106, 108, 118

0.45 m, PVDF
130

0.45 m, PVDF
130
Tricorn 5/50
107, 145

0.45 m, PVDF
130
U
UNICORN start software
143
Puradisc FP 30 Syringe Filter,

0.2 m, CA
130
UNICORN 5 software
143
Puradisc FP 30 Syringe Filter,

0.45 m, CA
130
UNICORN 6 software
143
X
XK 16/20 column
Q
99, 101, 122, 163
29, 122123, 162
29, 7576, 81,

123124, 162
Q Sepharose XL
29, 9192, 94, 97, 122,

162163
R
RESOURCE Q
29, 66, 6871, 161
RESOURCE S
6870, 126, 157, 161
68, 77, 85, 92, 94,

99, 165
XK 16/40 column
106
XK 16/60 column
120
XK 16/70 column
145
XK 26/20 column
68, 77, 85, 92, 99, 165
XK 26/40 column
68, 77, 85, 92, 99
XK 50/20 column
85, 92, 99, 165
XK 50/30 column
85, 92, 99
11000421 AC 167
GE Healthcare
Ion Exchange Chromatography Principles and Methods
www.gelifesciences.com
GE, GE monogram, Amersham, KTA, AxiChrom, Biacore, BioProcess, Capto, Cy, CyDye, ECL, ECL Plex,
ECL Select, FineLINE, HiPrep, HiScale, HiScreen, HiTrap, Hybond, MabSelect SuRe, MiniBeads, Mini Q,
Mini S, MiniTrap, MonoBeads, Mono Q, Mono S, PhastGel, PhastSystem, PreDictor, PrimeView, Protran,
ReadyToProcess, RESOURCE, Sephadex, Sepharose, SOURCE, SPARTAN, Superdex, Tricorn, UNICORN,
and Whatman are trademarks of General Electric Company.
Coomassie is a trademark of Thermo Fisher Scientific LLC, Gyrolab is a trademark of Gyros AB.
RoboColumn is a trademark of Atoll GmbH. Triton is a trademark of Union Carbide Chemicals and
Plastic Company Inc. Tween is a trademark of Croda Group of Companies. All other third-party
trademarks are the property of their respective owners.
GE Healthcare Bio-Sciences AB
Bjrkgatan 30
751 84 Uppsala
Sweden
The purchase of CyDye products includes a limited license to use the CyDye products for internal
research and development but not for any commercial purposes. A license to use the Cy and CyDye
trademarks for commercial purposes is subject to a separate license agreement with GE Healthcare.
Commercial use shall include:
1. Sale, lease, license or other transfer of the material or any material derived or produced from it.
2. Sale, lease, license or other grant of rights to use this material or any material derived or produced
from it.
3. Use of this material to perform services for a fee for third parties, including contract research and
drug screening.
Ion Exchange
Chromatography
If you require a commercial license to use the Cy and CyDye trademarks please contact: [email protected].
20042016 General Electric Company. First published Apr. 2004.
All goods and services are sold subject to the terms and conditions of sale of the company within
GE Healthcare that supplies them. A copy of these terms and conditions is available on request.
Contact your local GE Healthcare representative for the most current information.
GE Healthcare UK Ltd, Amersham Place, Little Chalfont, Buckinghamshire, HP7 9NA, UK
GE Healthcare Bio-Sciences Corp. 100 Results Way, Marlborough, MA 01752, USA
GE Healthcare Dharmacon, Inc., 2650 Crescent Dr., Lafayette, CO 80026, USA
HyClone Laboratories, Inc., 925 W 1800 S, Logan, UT 84321, USA
GE Healthcare Europe GmbH, Munzinger Strasse 5, D-79111 Freiburg, Germany
GE Healthcare Japan Corporation, Sanken Bldg. 3-25-1, Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
imagination at work
imagination at work
For local office contact information, visit www.gelifesciences.com/contact
11000421 AC 01/2016
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GE Healthcare

Ion Exchange Chromatography Principles and Methods

For local office contact information, visit www.gelifesciences.com/contact

Handbooks from GE Healthcare Life Sciences

2-D Electrophoresis using

GST Gene Fusion System

Nucleic Acid Sample

Nucleic Acid Sample

Principles and Methods

Principles and Methods

Instrument Management Handbook

Principles and Methods

Principles and Methods

Biacore Assay Handbook

Biacore Sensor Surface

Principles and Methods

Methodology and applications

Strategies for Protein

Cell Separation Media

Microcarrier Cell Culture

Cell Separation Media

Principles and Methods

Principles and Methods

Size Exclusion Chromatography

Ion Exchange Chromatography

Elution of target protein.....................................................................................................................................39

Sepharose High Performance: purification with high resolution .........................................................75

Ion exchange chromatography (IEX)

Size exclusion chromatography (SEC), also called gel filtration (GF)

Hydrophobic interaction chromatography (HIC)

Biorecognition (ligand specificity)

Affinity chromatography (AC)

Fig I.1. Separation principles in chromatographic purification.

Common acronyms and abbreviations

UV absorbance at specified wavelength (in this example, 280 nm)

anion exchange chromatography

bovine serum albumin

current good manufacturing practice

Chinese hamster ovary

cation exchange chromatography

capture, intermediate purification, polishing

domain antibody, the smallest functional entity of an antibody

desalting (group separation by size exclusion chromatography;

ethylene diaminetetraacetic acid

ethylene glycol-O,O-bis-[2-amino-ethyl]-N,N,N,N,-tetraacetic acid

enzyme-linked immunosorbent assay

fragment with two antigen binding sites, obtained by pepsin digestion

antigen binding fragment obtained by papain digestion

crystallizable fragment obtained by papain digestion

unstable fragment containing the antigen binding domain

gel filtration; also called size exclusion chromatography

host cell protein

hydrophobic interaction chromatography

high molecular weight

human serum albumin