Introduction to Mass

Spectrometry

March 2008
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that
weighs molecules !
0 units
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that
weighs molecules !
12 units
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that
weighs molecules !
12 units
8 9 10 11 12 13 14 15 16
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that
weighs molecules !
14 units
8 9 10 11 12 13 14 15 16
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that
weighs molecules !
12 units
8 9 10 11 12 13 14 15 16
mass
N
u
m
b
e
r

o
f

c
o
u
n
t
s

Outline
Basic Chemistry
Analytical Chemistry
Mass Spectrometry
Types of Ion Sources
EI, CI, ESI, APCI, APPI, MALDI
Types of MS
Ion Traps, Quads, FT-ICR, TOF, Sector
MS/MS
Performance Comparisons
Market Segments
Basic Chemistry
Everything is made of Atoms
Atoms are made of protons, neutrons, and
electrons
Many atoms together make up molecules
U
ATOM
Carbon
Oxygen
Hydrogen
Nitrogen
6 protons (+)

6 neutrons

6 electrons(-)
Carbon Atom
Carbon
More Carbon
6 protons (1 mass unit each) + 6 neutrons
(1 mass unit each) = 12 mass units
Electrons are negligible ( 1/3600 of mass unit)

Some carbon (about 1%) has 7 neutrons
so weigh 13 units

12.00 x 99%+13.00 x 1% = 12.01 amu
But how much does
an atom weigh ?
It was found that 12 grams of carbon
contains 6.02 x 10
23
atoms of carbon.
( 10
23
seconds have not elapsed since the beginning of time !)

So one atom of carbon weighs
1.99 x 10
-23
grams !



Caffeine

C
8
H
10
N
4
O
2

Total Mass
194 Daltons
3.22x10
-22
grams




N
N
C H
3
CH
3
N
N
CH
3
O
O
H
Caffeine

C
8
H
10
N
4
O
2

Total Mass
194 Daltons
3.22x10
-22
grams




N
N
C H
3
CH
3
N
N
CH
3
O
O
H
So we must devise a machine which
can measure ~ 10
-22
grams.
Analytical Chemistry
Instrumental Methods
Chemical Methods
Titration
Gravimetric Analysis
Solution Chemistry
Spectroscopy
Mass Spectrometry
Optical Absorption
NMR
Microwave
Optical Emission
FT-ICR
TOF
Quadrupole
Ion Trap
Linear Trap
Magnetic Sector
Gas Phase/
Ionize
Detector
Separate Based on
Mass/Charge
Sample
3 Elements to Mass Spectrometry
(J.J. Thomson ~ 1910)
Why Ionize ?
Difficult to manipulate
neutral particles on
molecular scale. If they are
charged, then we can use
electric fields to move them
around.
Gas Phase/
Ionize
Detector
Separate Based on
Mass/Charge
Sample
3 Elements to Mass Spectrometry
(J.J. Thomson ~ 1910)
Electron Impact (EI)
Chemical Ionization (CI)
Electrospray (ESI)
Atmospheric Pressure Chemical
Ionization (APCI)
Photo-ionization (APPI)
Matrix Assisted Laser Desorption
and Ionization (MALDI)
Gas Phase/
Ionize
Detector
Separate Based on
Mass/Charge
Sample
3 Elements to Mass Spectrometry
(J.J. Thomson ~ 1910)
Scanning (Filter)
Linear Quadrupole
Sector
Pulsed (Batch)
Ion Trap
FT-ICR
Time-of-Flight


Gas Phase/
Ionize
Detector
Separate Based on
Mass/Charge
Sample
3 Elements to Mass Spectrometry
(J.J. Thomson ~ 1910)
Faraday Cup
Discrete Dynode
Continuous Dynode
Multi-channel Plate



Gas Phase/
Ionize
Detector
Separate Based on
Mass/Charge
Sample
3 Elements to Mass Spectrometry
(J.J. Thomson ~ 1856-1940)
So, we could come up with 6x5x4 =
120 Unique Mass Spectrometers.

In reality, not all combinations make
sense, but many extra hybrid MS
systems have value. For example
Q-TOFs and LT-FT-ICR
6 Types of Ion Sources
Ion Source Depends on Sample
Solid Sample Liquid Sample Gas Sample
EI CI APCI MALDI ESI APPI
Make into Solution ? Make into Solid ? Turn into Gas?
Chemical
Properties
of analyte in gas
phase ?
Chemical
Properties
of analyte in
solution phase ?
Polarity, MW and Volatility
Polarity, MW and Volatility
Caffeine
Gas Phase Ionization
EI and CI are gas phase ionization
techniques
Sample is heated to cause
volatilization
The molecule must have a low
enough MW and polarity so that:


T
Boil
< T
Decomposition

Electron Impact
M
e-
e-
e-
M
(g)
+ e
-
M
+
(g)
+ 2e
-

This reaction creates the molecular ion so is very
useful.
However, the excess energy from the electron can
cause the molecular ion to fall apart:
s
0

s
1

IP
s
0

s
1

IP
2

Neutral
Molecule
Ionized
Molecule
Excess Energy
get redistributed
throughout ion
to cause
fragmentation.
Electron Impact
A
+
M
e-
e-
e-
M
(g)
+ e
-
M
+
(g)
+ 2e
-
M
+
(g)
A
+
Fragment 1 (g)
+ B
Fragment 2 (g)
Electron energy is chosen by compromise.
Fragment Information is useful. It can help structural
determination. However, many ions produce only
fragments with no molecular ion remaining. Molecular ion
often very unstable.
70 eV Classical Spectra to be used for comparisons
B B
N
N
C H
3
CH
3
N
N
CH
3
O
O
H
MW 194
N
N
C H
3
CH
3
N
N
CH
3
O
O
H
109 m/z
N
N
C H
3
CH
3
N
N
CH
3
O
O
H
55 m/z
Chemical Ionization
EI is not appropriate for some molecules
(it causes too much fragmentation)
Instead, ionize a reagent gas (by EI) then
react it with a analyte molecules
Typically use methane or ammonia for
reagent gas
CI: Form Reagent Ions First
For Example - Methane CI
1. electron ionization of CH4:
CH
4
+ e- CH
4
+
+ 2e
-
Fragmentation forms CH
3
+
, CH
2
+
, CH
+

2. ion-molecule reactions create stable reagent
ions:
CH
4
+
+ CH
4
CH
3
+ CH
5
+
CH
3
+
+ CH
4
H
2
+ C
2
H
5
+

CH
5
+
and C
2
H
5
+
are the dominant methane CI reagent
ions
Methane CI Reagent Ions
Ions at m/z 17, 29, and 41 are from methane;
H
3
O
+
is also formed from water vapor in the
vacuum system
Reagent Ions React with Analytes
Several Types of Reactions May Occur
Form Pseudomolecular Ions (M+1)
CH
5
+
+ M CH
4
+ MH
+

M+1 Ions Can Fragment Further to Produce a Complex CI
Mass Spectrum
Form Adduct Ions
C
2
H
5
+
+ M [M + C
2
H
5
]
+
M+29 Adduct
C
3
H
5
+
+ M [M + C
3
H
5
]
+
M+41 Adduct
Molecular Ion by Charge Transfer
CH
4
+
+ M M
+
+ CH
4
Hydride Abstraction (M-1)
C
3
H
5
+
+ M C
3
H
6
+ [M-H]
+
Common for saturated hydrocarbons
EI Spectrum of Cocaine
Extensive Fragmentation
Molecular Ion is Weak at m/z 303
Methane CI of Cocaine
Pseudo molecular Ion and Fragment Ions
Isobutane CI of Cocaine

Soft Reagent - Less Fragmentation

Polarity, MW and Volatility
Liquid Techniques
Depending on solvent composition and
molecular properties either
APPI
ESI
APPI
APPI
Lamp Wavelength
chosen to only excite
analytes not
solvent/background
Low amount of
photo dissociation
results
New technique with
few novel
applications
Less universal than
electrospray
APPI
APCI Principles
Rapidly vaporize entire liquid flow
Ionize solvent molecules in corona
discharge
CI process ionizes sample molecules
Positive mode: proton transfer or charge
exchange
Negative mode: proton abstraction or
electron capture
APCI Cut Away View
What applications
need APCI?
APCI works well for small molecules that are
moderately polar to non-polar
APCI works well for samples that contain
heteroatoms
Avoid samples that typically are charged in
solution
Avoid samples that are very thermally unstable
or photosensitive
Why Electrospray ?
Most Samples are delivered as liquids.
GC analysis requires heating sample to cause
evaporation
Ionization occurs through electron impact or
chemical reaction
Not all analytes are thermally stable
Electrospray was designed to provide a
gentle method of creating gas phase ions
Three Step Process
1)Droplet formation
2)Droplet Shrinkage
3)Gaseous Ion Formation
Electrospray process does not ionize samples !
Taylor Cone
Solutions delivered to the tip of the electrospray capillary
experience the electric field associated with the
maintenance of a high potential.
Assuming a potential gradient, positive ions will
accumulate at the surface.
Positively Charged Ions will bud off the surface when the
applied electrostatic force is bigger than the surface tension.
Assisted Electrospray
Nebulizing
Gas
LC Column Flow
High Voltage (5 kv) Low Voltage (0.5 kv)
MS
Drying
Gas
Low Voltage (0.1 kv)
MALDI
Matrix Assisted Laser Desorption Ionization
Analyte co-deposited with Matrix
Laser excites matrix which transfers energy to analyte
Produces singly charged species
Typically used for large biomolecules / polymers
MALDI is a high mass/pulsed source so usually
combined with TOF
5 Types of Mass
Spectrometers
5 Types of Mass Spectrometers
Scanning (Filter)
Linear Quadrupole
Sector
Pulsed (Batch)
Ion Trap
FT-ICR
Time-of-Flight


( Separation in Space)
( Separation in Time)
Basics of Ion Physics
ma F =
qE F =
qV mv E K = =
2
2
1
. .
m mass
a acceleration
B Magnetic Field
q charge
E - electric field
F Force
K.E. kinetic energy
V electric potential
v - velocity
qvB F =
Combine 1
st
two equations
qE ma =
m
qE
a

=
m
qE
a

=
We can
control this.
(volts/meter)
We can
measure
this.
m
qE
a

=
We can
control this.
(volts/meter)
We can
measure
this.
We can deduce This !
0V
-40V
+
0V
-40V
+
1 meter
m
qE
a

=
Time of Flight MS
qV mv E K = =
2
2
1
. .
2
2
2
l
Vt
q
m
=
Time of Flight (TOF)
+ Very high mass range
+ Both high resolution and high
sensitivity
+ Mass accuracy
+ High scan speed
+ Mechanically simple
m/z t
2

- High vacuum critical
- Demanding high voltage/ pulsed/ high
precision electronics
- Expensive
Bruker, Waters-Micromass, JEOL, Analytica
Time of Flight
SECTOR MS
qvB
r
mv
F = =
2
v
r B
q
m
2
2 2
=

High resolution (60,000 at 10% valley).
MStation Double Focusing Magnetic Sector Mass Spectrometer
FROM JEOL
Very high reproducibility
Best quantitative performance of all mass
spectrometer analyzers
High resolution
High sensitivity
High dynamic range
- Large
- Expensive
- Not suited for pulsed sources
FT-ICR
qvB
r
mv
F = =
2
m
qB
r
v
= = e
1347.734
1348.736
1349.741
m
m
A
= Resolution
PROFILE Scan 35 from ...ta sept 24.04\0.01+0.036 extrste mode 1 609.xms
605.0 607.5 610.0 612.5 615.0 617.5
m/z
0.0
0.5
1.0
1.5
kCounts
609.50
0.3541
1384
610.45
0.4533
471
611.45
0.3952
114
PROFILE Spectrum 1A
0.472 min. Scans: 3-67 Channel: 1 Ion: 2000 us RIC: 21543 BP 609.50 (1384=100%) 0.01+0.036 extrste mode 1 609.xms
609
607
610
611
612
Reserpine
Reserpine is used to treat high blood pressure. It works by decreasing your heart rate
and relaxing the blood vessels so that blood can flow more easily through the body.
It also is used to treat severe agitation in patients with mental disorders
Resolution ~ 1200

LC/MS/MS with data dependent acquisition using
Brukers simple, unified Compass software package

Exact mass MS analysis to sub-ppm levels for
unambiguous determination of elemental chemical
composition. Automated software to confirm
composition with m/z and isotopic pattern information

Exact mass MS(n) capability for detailed structural
analysis and peptide sequencing

Qh-hybrid along with CID and ECD for top-down
proteomics (TopPro) facilitates selected gas phase
ion enrichment

Extreme resolution capability for direct analysis of
complex mixtures (> 600,000 FWHM)

Wide m/z range simultaneous detection of ions (e.g.
100 - 7,000 m/z)

Sub fmol sensitivity
FT-ICR
The highest recorded mass resolution of
all mass spectrometers
Powerful capabilities for ion chemistry
and MS/MS experiments
Well-suited for use with pulsed ionization
methods such as MALDI
Non-destructive ion detection; ion
remeasurement
Stable mass calibration in
superconducting magnet FTICR systems
Limited dynamic range
High Vacuum Demands
Subject to space charge effects and ion molecule
reactions
Many parameters (excitation, trapping, detection
conditions) comprise the experiment sequence that
defines the quality of the mass spectrum
Generally low-energy CID, spectrum depends on
collision energy, collision gas, and other parameters
Ion Traps, Transmission
Quadrupoles and Linear Traps
Electrodynamic quadrupole fields
Paul (University of Bonn in 1953 Nobel Prize 1989)
3D and 2D traps
Created a high resolution quad that was 5.82 m
long !
A quadrupole field is linearly dependant on the
coordinate axis
Ions are confined or rejected based on Voltage,
Frequency, Dimension, Mass and Charge
Ion Traps and Quads

Traps are Pulsed
Quads are Continuous
Both rely time varying
electric fields (RF)


+
+
+
-
-
+
+
+
-
-
+
+
+
-
-
Splat
+
-
-
+
+
+
-
-
+
+
+
-
-
+
+
+
+
+
-
-
Forces on ion are simple to understand
As always

Where F
z
= the force in the z direction
e = charge on the particle
m = mass of the particle
a = acceleration
E
z
= electric field
ma eE F
z z
= =
Ion Trap + Quadrupole Theory
z
e
dt
z d
m ma F
z Z
c
c
= = =
|
2
2
) cos (
2
2 2
2
t V U
r
z e
dt
z d
m ma F
o
Z
O = = =
z z
eE ma F = =
0 ) cos (
2
2 2
2
= O z t V U
m r
e
dt
z d
o
0 ) cos (
2 2
2
= O + r t V U
m r
e
dt
r d
o



Ion Motion in an Ion Trap
After several pages of math, we can derive an equation
for ion motion as a function of time:
These second order differentials are not trivial to solve.
Mathieu Equation ! ( solved in 1868 , sub type of Hills
equations)
Graphical Solution (Slightly different for Traps and
Quads because of symmetry.)

NEED SOLUTIONS WHICH ARE BOUND AND STABLE IN
TIME
Stable Solutions to the Mathieu Equation
For a Quadrupole
2 2 2 2
z
m
4eV -

m
8eU -
a
o
z
o
r
q
r O
=
O
=
Mathieu Equation for an ion trap

a
u
q
u
15
-15
15
5 10
10
5
0
-5
-10
20 25
z stable
z stable
r stable
r stable
a
u
q
u
15
-15
15
5 10
10
5
0
-5
-10
20 25
z stable
z stable
r stable
r stable
2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
a
z
q
z
|
z
|
r
1.4 1.2 0.8 0.6 0.4 0.2 1.0
1.0
0.8
0.6
0.4
0.0
0.2
0.4
0.6
0.8
1.0
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
a
z
q
z
|
z
|
r
1.4 1.2 0.8 0.6 0.4 0.2 1.0 1.4 1.2 0.8 0.6 0.4 0.2 1.0
1.0
0.8
0.6
0.4
0.0
0.2
0.4
0.6
0.8
1.0
Operated in RF only
mode
Light ions have a
higher q
z
than heavier
ions
Ions stable in z axis
when q
z
< 0.908
Ions selectively
ejected when RF
amplitude is raised
Light ions leave first,
heavier ions later
2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
Stability Diagram ( Area 1)
Stability Diagram for a Quad
2 2 2 2
z
m
4eV -

m
8eU -
a
o
z
o
r
q
r O
=
O
=
Stability Diagram for a Quad
2 2 2 2
z
m
4eV -

m
8eU -
a
o
z
o
r
q
r O
=
O
=
200
100
50
V=200V
U=0V
Stability Diagram for a Quad
2 2 2 2
z
m
4eV -

m
8eU -
a
o
z
o
r
q
r O
=
O
=
V=200V
U=50V
200
100
50
Stability Diagram for a Quad
2 2 2 2
z
m
4eV -

m
8eU -
a
o
z
o
r
q
r O
=
O
=
V=200V
U=100V
100
200
50
Stability Diagram for a Quad
2 2 2 2
z
m
4eV -

m
8eU -
a
o
z
o
r
q
r O
=
O
=
150
200
50
V=400V
U=200V
Stability Diagram for a TRAP
Quad operates by
selectively passing
one m/z at a time.


Trap operates by
collecting all ions
simultaneously and
then ramping them
out one at a time.

2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
a
z
q
z
|
z
|
r
1.4 1.2 0.8 0.6 0.4 0.2 1.0
1.0
0.8
0.6
0.4
0.0
0.2
0.4
0.6
0.8
1.0
0.1
0
- 0.1
- 0.2
- 0.3
- 0.4
- 0.5
- 0.6
a
z
q
z
|
z
|
r
1.4 1.2 0.8 0.6 0.4 0.2 1.0 1.4 1.2 0.8 0.6 0.4 0.2 1.0
1.0
0.8
0.6
0.4
0.0
0.2
0.4
0.6
0.8
1.0
Stability Diagram for a Trap
2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
200
100
50
V=200V
U=0V
Eject when q=0.908
Stability Diagram for a Trap
2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
200
100
50
V=300V
U=0V
Eject when q=0.908
Stability Diagram for a Trap
2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
200
100
50
V=400V
U=0V
Eject when q=0.908
Mass Spectrum on a Quad or Trap
Ramp RF (in trap) or ramp RF/DC in Quad
RF
Spectrum
2 2 2 2
z
m
8eV -

m
16eU -
a
o
z
o
r
q
r O
=
O
=
Stability Diagram for a Trap
? = m
Potential Well Model
Need for helium buffer gas
2 2
2
4
2
O

= =
o
r z
mz
eV
D D
2 2 2
2
1
2
O
|
|
.
|

\
|
+ =
O
=
u
u u u
q
a | e
Secular Frequency
Ion Motion in Trap contains many frequency
components
These depend on a and q parameters
(When q < 0.40)

0 0.2 0.4 0.6 0.8 1
m/z= 500
q = 0.1816
= 50.5 kHz
m/z= 1000
q = 0.0908
= 25.1 kHz
m/z= 1500
q = 0.0605
= 16.7 kHz
Low Mass
Cut Off
100 m/z
m/z= 106
q = 0.850
= 301.9 kHz
0 0.2 0.4 0.6 0.8 1
m/z= 500
q = 0.1816
= 50.5 kHz
m/z= 1000
q = 0.0908
= 25.1 kHz
m/z= 1500
q = 0.0605
= 16.7 kHz
Low Mass
Cut Off
100 m/z
m/z= 106
q = 0.850
= 301.9 kHz
Varian Eject
frequency
Amplitude
Fourier Transform
Notched Broad Band Waveform
0 0.2 0.4 0.6 0.8 1
m/z= 500
q = 0.1816
= 50.5 kHz
m/z= 1000
q = 0.0908
= 25.1 kHz
m/z= 1500
q = 0.0605
= 16.7 kHz
Low Mass
Cut Off
100 m/z
m/z= 106
q = 0.850
= 301.9 kHz
Frequency Notch
180kHz 240kHz
Practical Mass Spectrometer
Load Time
Ion Ejection
Notched
Waveform
Dipole Ejection
Mass Spectrum
Ion trap
Benefits
High sensitivity
Multi-stage mass spectrometry
(analogous to FTICR
experiments)
Compact mass analyzer
Cheap and Easy to build
Limitations
Poor quantitation
Poor inherent dynamic range
Subject to space charge effects and ion
molecule reactions
Collision energy not well-defined in CID
MS/MS
Many parameters (excitation, trapping,
detection conditions) comprise the
experiment sequence that defines the quality
of the mass spectrum

Transmission Quadrupole Mass Spectrometer
Benefits
Classical mass spectra
Good reproducibility
Relatively small and low-cost
systems
Potentially good conversion
efficiency for MS/MS

Limitations
Limited resolution
Peak heights variable as a function of
mass (mass discrimination). Peak height
vs. mass response must be 'tuned'.
Not well suited for pulsed ionization
methods
Low-energy collision-induced
dissociation (CID) MS/MS spectra in triple
quadrupole and hybrid mass
spectrometers depend strongly on
energy, collision gas, pressure, and other
factors.

Linear Trap
+ =
Newest Generation MS
Many of the advantages of ion
traps, without normal trap
limitations.
Less Space Charge Problems
MS
N
Great loading Efficiency

MS/MS
In a transmission Quadrupole, MS/MS is
done in Space
need three quads ( Triple Quad)
In an Ion trap MS/MS is done in time.
Pass only 195
RF ONLY
-Pass
Everything
-Collisions with
Ar cause
fragmentation
Scan from 100-195
Look at daughter ions
Q1
Q2 Q3
vs.
Triple
Quad
Ion
Trap
Why MS/MS
Unknown Identification
Potentially two compounds of interest
have the same mass ( and same retention
time)
Quantitation improvements ( background
signal reduced)
Problem: Thiabendazole in
Grapefruit Extract
Antifungal agent, thiabendazole (TBZ) must be
below 10 ppb in the processed grapefruit
Major matrix interferent:
Similar retention time
Similar spectrum
Concentration much greater than TBZ

Interferent
Interferent
MS, MS/MS, and MS/MS/MS of TBZ
Matrix peak
Matrix peak
No matrix peak
MS (500 pg)



MS/MS (10 pg)



MS/MS/MS (10 pg)
20180-220
20117465-220
Select
Scanning
Product Ion Scan
Select
Precursor ion Scan
Scanning
Neutral Loss Scan
Scanning
Scanning
Quadrupole 1
MS 1
Quadrupole 2
Collision Cell
Quadrupole 3
MS 1
Real Life System
PROFILE Scan 35 from ...ta sept 24.04\0.01+0.036 extrste mode 1 609.xms
605.0 607.5 610.0 612.5 615.0 617.5
m/z
0.0
0.5
1.0
1.5
kCounts
609.50
0.3541
1384
610.45
0.4533
471
611.45
0.3952
114
PROFILE Spectrum 1A
0.472 min. Scans: 3-67 Channel: 1 Ion: 2000 us RIC: 21543 BP 609.50 (1384=100%) 0.01+0.036 extrste mode 1 609.xms
609
607
610
611
612
Reserpine
Reserpine is used to treat high blood pressure. It works by decreasing your heart rate
and relaxing the blood vessels so that blood can flow more easily through the body.
It also is used to treat severe agitation in patients with mental disorders
PROFILE Scan 85 from ...ultip charge ions\4500-cytochrome c-6-17-04.xms
500 750 1000 1250 1500 1750 2000
m/z
0.0
0.5
1.0
1.5
2.0
2.5
kCounts
721.00
1.3347
238
765.65
0.6099
1186
816.43
0.3790
2316
874.45
0.4061
1507
941.55
0.4655
693
1020.13
0.4678
413
1112.72
0.4881
247
1223.87
0.6065
183
1359.76
0.5506
236
1529.57
0.5139
456
1747.75
0.7672
180
PROFILE Spectrum 1A
4.898 min. Scans: 10-160 Channel: 1 Ion: 500 us RIC: 159835 BP 816.43 (2316=100%) 4500-cytochrome c-6-17-04.xms
Cytochrome C MW 12220
+17
+16
+15
+14
+13
+12
+11
+10
+9
+8
+7
m/z = mass/charge
(

+
+
+
nH
nH MW
Market Segments and Where
Varian Sits
73%
4%
18%
3%
2%
Single Quadrupole
$204 M
Triple Quadrupole
$ 14 M
Ion Trap
$50 M
Sector
$5 M
TOF
$7 M
GC/MS mass analyzer type
GC/MS Initial Sales $280M
18%
33%
25%
8%
3%
13%
Single Quadrupole
$114 M
Triple Quadrupole
$221 M
Ion Trap
$140 M
Sector/FTICR
$30 M
Q-TOF
$128 M
API TOF
$65 M
LC/MS mass analyzer type
2004 LC/MS Initial Sales $698M
Agilent Bruker JEOL Micro
Mass
Sciex Thermo Varian
Single Quad
1 2 1 1 1
Triple Quad
2 4 4 1
Sector
3 1 1
FT-ICR
2 1
3D Trap
3 3 2 1
Linear Trap
1 1
TOF

1 1 1 2
TOF/TOF

2
Q-TOF

2 4 1
TOTAL (LC/MS) 5 10 4 11 6 10 3
The High-end LC/MS Vendors
High-end TQ (55%)
Waters, Thermo, ABI

High-end Ion Traps (23%)
Bruker/Agilent, Thermo

LTQ -Thermo

LC-TOF, TOF-TOF, Q-
TOF (13%)
Q-Trap (5%)
Magnetic sector (4%)


High-end LC/MS Vendor Market Share
Markets served by the high-end LC/MS

Academic, Food/AG, Indep.Test
40M (5%) 14M (15%) 16M (6%)





Total Market $330M
Varian participates in less than 25% of the market, with a 1% overall market share
What is a Mass Spectrometer?
A Mass Spectrometer is a machine that
weighs molecules ! (by measuring the
mass to charge ratio of ions)
Source
EI
CI
ESI
APCI
APPI
MALDI

Dispersion
TOF
FT-ICR
Sector
Quad
Trap
Detector
Faraday Cup
Channeltron
MCP