CHAPTER

HRMS: Fundamentals and

Basic Concepts

Franciso Javier Arrebola-Liébanas, Roberto Romero-González,

1
Antonia Garrido Frenich
University of Almerı´a, Almerı´a, Spain

1.1 INTRODUCTION (TO HIGH-RESOLUTION MASS

SPECTROMETRY)
1.1.1 BASIC CONCEPTS (UNITS AND DEFINITIONS)
Mass spectrometry (MS) is an analytical technique commonly used for qualitative
and quantitative chemical analysis. MS measures the massecharge ratio (m/z) of
any analyte, of both organic and inorganic nature, which has previously been
ionized. Only the ions are registered in MS, but the particles with zero net electric
charge (molecules or radicals) are not detected. Therefore, MS does not directly
measure mass, but it determines the m/z, being m the relative mass of an ion on
the unified atomic scale divided by the charge number, z, of the ion (regardless of
sign). The m/z value is a dimensionless number.
Because the mass of atoms and molecules is very small, the kilogram as standard
international (SI) base unit cannot be used for its measurement. For that, a non-SI
unit of mass, unified atomic mass unit (u) is used. At this point, in this introductory
section, it is worth clarifying some basic terms (units and definitions) in MS accord-
ing to the International Union of Pure and Applied Chemistry (IUPAC) recommen-
dations (IUPAC, 1997; Murray et al., 2013).
The u also called Dalton (Da), is defined as 1/12th of the mass of one atom of 12C
at rest in its ground state, being 1 u ¼ 1 Da ¼ 1.660538921 (73)  1027 kg (num-
ber in parentheses indicates the estimated uncertainty). In this way, the mass of other
atoms or molecules is expressed relative to the mass of the most abundant stable
isotope of carbon, 12C, and this value is dimensionless.
The z is defined as absolute value of charge of an ion divided by the value of the
elementary charge of the electron (e) rounded to the nearest integer, being
e ¼ 1.602177  1019 C. The m/z unit is the thomson (Th), although it is now a
deprecated term, being 1 Th ¼ 1 u/e ¼ 1.036426  108 kg/C. For that, use of the
dimensionless term m/z is accepted in the literature, and this criterion will be fol-
lowed throughout this book.
Other basic concepts that are commonly used in MS will be shortly described to
clarify the meaning of these throughout the following chapters.

Applications in High Resolution Mass Spectrometry. http://dx.doi.org/10.1016/B978-0-12-809464-8.00001-4 1

Copyright © 2017 Elsevier Inc. All rights reserved.
2 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

• Atomic mass: The number that represents the element’s mass based on the
weighted average of the masses of its naturally occurring stable isotopes. For
example, the integer atomic mass of bromine is 80 Da. This is because there are
only two naturally occurring stable isotopes of bromine, 79Br and 81Br, which
exist in nature in about equal amounts. When the relative mass (Mr) of an ion,
molecule, or radical is reported, it is based on the atomic masses of its elements.
• Nominal mass: Mass of a molecular ion or molecule calculated using the isotope
mass of the most abundant constituent element isotope of each element
(Table 1.1) rounded to the nearest integer value and multiplied by the number
of atoms of each element. Example: nominal mass of H2O ¼ (2  1 þ 1  16)
u ¼ 18 u.
• Monoisotopic mass: Exact mass of an ion or molecule calculated using the mass
of the most abundant isotope of each element. Example: monoisotopic mass of
H2O ¼ (2  1.007825 þ 1  15.994915) u ¼ 18.010565 u. The exact mass of
the common elements and their isotopes are provided in Table 1.1.
• Exact mass: Calculated mass of an ion or molecule with specified isotopic
composition.
• Mass defect: Difference between the nominal mass and the monoisotopic mass of
an atom, molecule, or ion. It can be a positive or negative value.
• Relative isotopic mass defect (RDm): It is the mass defect between the mono-
isotopic mass of an element and the mass of its Aþ1 or its Aþ2 isotopic cluster
(Thurman & Ferrer, 2010). For instance, RDm for the pair 35Cl:37Cl is
0.0030 Da.
• Average mass: Mass of an ion or molecule weighted for its isotopic composition,
i.e., the average of the isotopic masses of each element, weighted for isotopic
abundance (Table 1.1). Example: average mass of
H2O ¼ (2  1.00794 þ 1  15.9994) u ¼ 18.01528 u.
• Accurate mass: Experimentally determined mass of an ion of known charge.
• Mass accuracy: Difference between the mass measured by the mass analyzer and
theoretical value.
• Resolution or mass resolving power: Measure of the ability of a mass analyzer to
distinguish two signals of slightly different m/z ratios.
• Mass calibration: Means of determining m/z values of ions from experimentally
detected signals using a theoretical or empirical relational equation. In general,
this is accomplished using a computer-based data system and a calibration file
obtained from a mass spectrum of a compound that produces ions of known m/z
values.
• Mass limit: Value of m/z above or below which ions cannot be detected in a mass
spectrometer.
• Mass number: The sum of the protons and neutrons in an atom, molecule, or ion.
If the mass is expressed in u, mass number is similar to nominal mass.
• Most abundant ion mass: The mass that corresponds to the most abundant peak
in the isotopic cluster of the ion of a given empirical formula.
 1.1 Introduction (To High-Resolution Mass Spectrometry) 3

Table 1.1 Nominal, Isotopic, and Average Masses of Some Common Stable
Isotopes
Nominal Isotopic Average
Element Isotope Abundance Mass Mass Mass
1
H H 99.9885 1 1.007825 1.00794
2
H 0.0115 2 2.014102
12
C C 98.93 12 12.000000 12.0110
13
C 1.08 13 13.003355
14
N N 99.632 14 14.003074 14.00674
15
N 0.368 15 15.000109
16
O O 99.757 16 15.994915 15.9994
17
O 0.038 17 16.999131
18
O 0.205 18 17.999160
19
F F 100 19 18.998403 18.9984
23
Na Na 100 23 22.989770 22.9898
28
Si Si 92.2297 28 27.976927 28.0855
29
Si 4.6832 29 28.976495
30
Si 3.0872 30 29.973770
31
P P 100 31 30.973762 30.9738
32
S S 94.93 32 31.972072 32.0660
33
S 0.76 33 32.971459
34
S 4.29 34 33.967868
35
Cl Cl 75.78 35 34.968853 35.4527
37
Cl 24.22 37 36.965903
79
Br Br 50.69 79 78.918336 79.9094
81
Br 49.32 81 80.916289
127
I I 100 127 126.904476 126.9045

1.1.2 LOW-RESOLUTION MASS SPECTROMETRY VERSUS HIGH-

RESOLUTION MASS SPECTROMETRY
It should be noted that mass measurements in MS can be carried out at either low
resolution (LRMS) or high resolution (HRMS). An LRMS measurement provides
information about the nominal mass of the analyte (Dass, 2007), i.e., the m/z for
each ion is measured to single-digit mass units (integer mass). However, exact
mass is measured by HRMS, i.e., the m/z for each ion is measured to four to six
decimal points (Ekman, Silberring, Westman-Brinkmalm, & Kraj, 2009). This is
very useful to structure elucidation of unknown compounds for analytes having
the same nominal mass, but with very small differences in their exact masses. As
a result, by LRMS measurements it is not possible to differentiate between imazalil,
C14H14Cl2N2O (14  12 þ 14  1 þ 2  35 þ 2  14 þ 1  16 ¼ 296 u), and flu-
nixin, C14H11F3N2O2 (14  12 þ 11  1 þ 3  19 þ 2  14 þ 2  16 ¼ 296 u),
4 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

pesticides. However, this would be possible by using exact mass measurements,

imazalil C14H14Cl2N2O (14  12 þ 14  1.007825 þ 2  34.968852 þ 2 
14.003074 þ 1  15.994915 ¼ 296.048317 u) and flunixin C14H11F3N2O2 (14 
12 þ 11  1.007825 þ 3  18.998403 þ 2  14.003074 þ 2  15.994915 ¼
296.077262 u).
High-resolution mass spectrometers have evolved from the 1960s with the intro-
duction of double-focusing magnetic-sector mass instruments (Picó, 2015). Next,
Fourier transform ion cyclotron resonance (FT-ICR), time-of-flight (TOF), and Orbi-
trap mass analyzers were also introduced in the market. Also, hybrid HRMS instru-
ments, such as quadrupole TOF (Q-TOF), ion trap (IT)-TOF, linear trap quadrupole
(LTQ)-Orbitrap, or QeOrbitrap, have been developed. These last analyzers provide
tandem (MS/MS) or MSn spectra of high resolution, in addition to accurate mono-
isotopic mass measurements, of great applicability both for the confirmation of
target compounds and the identification of unknown compounds (Lin et al.,
2015). The TOF and Orbitrap analyzers, single or hybrid instruments, are the
most widely used in the analysis of organic contaminants, such as pesticide residues
(Lin et al., 2015; Picó, 2015).
Among the main characteristics that define the performance of a mass analyzer
are (Dass, 2007; de Hoffmann & Stroobant, 2007; Mcluckey & Wells, 2001) mass
range, speed, efficiency, linear dynamic range, sensitivity, resolution (or its mass
resolving power), and mass accuracy. The mass range is that over which a mass spec-
trometer can detect ions or is operated to record a mass spectrum. When a range of
m/z is indicated instead of a mass range, this should be specified explicitly. The
speed or scan speed is the rate at which the analyzer measures over a particular
mass range. Efficiency is defined as the product of the transmission of the analyzer
by its duty cycle, where the transmission is the ratio of the number of ions reaching
the detector and the number of ions entering the mass analyzer, and the duty cycle
can be described as the fraction of the ions of interest formed in the ionization step
that are subjected to mass analysis.
Linear dynamic range is considered as the range over which ion signal is linear
with analyte concentration. Sensitivity can be expressed as detection sensitivity or
abundance sensitivity; the first is the smallest amount of an analyte that can be
detected at a certain defined confidence level, while the second is the inverse of
the ratio obtained by dividing the signal level corresponding to a large peak by
the signal level of the background at one mass-to-charge unit lower or higher. A
summary of these characteristics of high-resolution mass analyzers is shown in
Table 1.2. As it can be observed, in terms of resolving power and accuracy, the
FT-ICR analyzer presents the best values, followed by the recently introduced tribrid
Orbitrap analyzer. TOF and Q-TOF analyzers have worse values, although the FT-
ICR analyzer comprises the worst sensitivity.
Last but not least, two key characteristics of high-resolution mass analyzers are
resolution (or its mass resolving power) and mass accuracy, which will be treated in
more detail in the following two sections.
 1.1 Introduction (To High-Resolution Mass Spectrometry)
Table 1.2 Comparison of the Characteristics of Some High-Resolution Mass Spectrometry Analyzers
Mass Linear Dynamic Resolving Power Accuracy
Analyzer Range Speed Range Sensitivity (FWHM) (ppm)
Magnetic sector 10,000 w1 s 109 106e109 100,000 <1
FT-ICR 10,000 w1 s 103e104 103e104 1,000,000 <1
TOF >300,000 Milliseconds 106 106 30,000 3e5
Q-TOF 10,000 wMilliseconds 103e104 106 30,000 3e5
IT-TOF w0.1 s 103e104 105 100,000 3e5
Exactive Orbitrap 4000 0.1 s >5000 106 100,000 <3
LTQ-Orbitrap 4000 0.1 s >5000 106 100,000/240,000 <3
Q-Orbitrap 8000 0.05 s 105 106 240,000 <2
Tribrid Orbitrap 6000 0.05 s 105 106e107 500,000 <1
FT-ICR, Fourier transform ion cyclotron resonance; FWHM, full width at half maximum; IT-TOF, ion trap TOF; LTQ, linear trap quadrupole; Q-TOF, quadrupole TOF;
TOF, time-of-flight. Adapted from Picó, Y. (2015). Advanced mass spectrometry. In Y. Picó (Ed.), Comprehensive analytical chemistry, Vol. 68. Amsterdam:
Elsevier.

5
6 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

1.2 RESOLUTION AND MASS RESOLVING POWER

Resolution or resolving power is the capacity of a mass analyzer to yield distinct sig-
nals for two ions with a small m/z difference (de Hoffmann & Stroobant, 2007). Un-
fortunately, there is confusion about these two concepts and also between mass
resolving power and resolving power in MS, because the definitions provided by
different documents are not exactly the same.
Dass (2007) defines the mass resolution of a mass spectrometer as its ability to
distinguish between two neighboring ions that differ only slightly in their mass
(Dm). According to this definition, it is the inverse value of the resolving power,
RP ¼ m/Dm, where m is the average of the accurate masses, (m1 þ m2)/2, of the
two neighboring ions. Xian, Hendrickson, and Marshall (2012) define the resolution
as the smallest mass difference, m2  m1 or Dm, between two mass spectral peaks
such that the valley between their sum is a specified fraction (e.g., 50%) of the
height of the smaller individual peak. A similar definition is given by Marshall,
Hendrickson, and Shi (2002), as the minimum mass difference between two equal
magnitude peaks such that the valley between them is a specified fraction of the
peak height.
The IUPAC recommendations (Murray et al., 2013) define resolution as m/Dm,
where m is the m/z of the ion of interest. Although depending on the method of mea-
surement of D(m/z), it is possible to differentiate between the two concepts (Murray
et al., 2013; Price, 1991). On one hand, resolution, as 10% valley, is the (m/z)/D(m/z)
value measured for two peaks of equal height in a mass spectrum at m/z and m/
z þ D(m/z) that are separated by a valley for which the lowest point is 10% of the
height of either peak, i.e., the peaks are resolved when the valley between the two
m/z values is 10% of the height of either one (Fig. 1.1). For peaks of similar height
separated by a valley, let the height of the valley at its lowest point be 10% of the
lower peak, and the resolution should be given for a number of values of m/z.
This 10% valley definition for the resolution is used with magnetic-sector analyzers
(Ekman et al., 2009).
On the other hand, resolution, as peak width, expresses the (m/z)/D(m/z) value for
a single peak, where D(m/z) is the width of the peak at a height, which is a specified
fraction (50, 5, or 0.5%) of its maximum peak height (Fig. 1.1). The used fraction is
often 50%, and D(m/z) is named as full width at half maximum (FWHM). FT-ICR,
TOF, and Orbitrap analyzers use this 50% valley definition for set resolution (Ekman
et al., 2009).
In addition, there is controversy in the definition of mass resolving power and
resolving power in MS (IUPAC, 1997). The definition of the first term is similar
to the definition of resolution indicated earlier (Murray et al., 2013), i.e., as a dimen-
sionless ratio between m/Dm. Resolving power in MS is the ability of an instrument
or measurement procedure to distinguish between two peaks differing in the quotient
m/z by a small increment and expressed as the peak width in mass units. However,
both terms have been unified in the current IUPAC definition as a measure of the
ability of a mass spectrometer to provide a specified value of mass resolution.
 1.3 Accurate Mass Measurement: Exact Mass and Mass Defect 7

FIGURE 1.1
Methods of calculating mass resolving power.
Reprinted from Picó, Y. (2015). Advanced mass spectrometry. In Y. Picó (Ed.), Comprehensive analytical
chemistry, Vol. 68. Amsterdam: Elsevier, with permission from Elsevier.

1.3 ACCURATE MASS MEASUREMENT: EXACT MASS AND

MASS DEFECT
It is important to differentiate between accurate mass and exact mass. The first is the
experimentally determined mass of an ion of known charge (Bristow and Webb,
2003; Sparkman, 2006) and it refers to a measured mass, while the second is the
calculated mass of an ion or molecule with specified isotopic composition (Kim,
Rodgers, & Marshall, 2006), and it refers to a calculated mass. Therefore, although
an LR mass spectrometer can measure integer relative mass with high accuracy, the
information obtained is not so complete as the measurement of accurate relative
mass offered by HR mass spectrometers (Herbert & Johstone, 2003). The difference
between the nominal mass and the monoisotopic mass of an atom, molecule, or ion,
positive or negative value, is the mass defect.
8 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

The value of accurate mass measurement is illustrated in the following examples:

(1) to distinguish compounds with the same integer nominal (molecular) mass in the
same sample; (2) to determine the molecular formula or elemental composition for
an unknown compound, which is helpful for its identification; and (3) to find out the
fragmentation routes. As an example, Fig. 1.2 shows the fragmentation pattern for
the flonicamid pesticide, which can be elucidated by HRMS.
In HRMS, the mass accuracy is the difference between the m/z value measured
by the mass spectrometer and the theoretical m/z value. It can be reported as an
absolute value; for instance, in millimass units (mmu) or millidalton (mDa):

Mass accuracyðmmuÞ ¼ ðm=zmeasured  m=ztheoretical Þ  103

Also, it can be expressed as a relative value in parts per million (ppm):
 
m=zmeasured  m=ztheoretical
Mass accuracyðppmÞ ¼ 106
ðm=ztheoretical Þ

FIGURE 1.2
Fragmentation pattern for the flonicamid pesticide (TFNA: 4-trifluoromethylnicotinic acid;
TFNA-AM: 4-trifluoromethilnicotinamide).
 1.4 Mass Calibration in High-Resolution Mass Spectrometry 9

In general, an acceptable value of the measured mass should be within 5 ppm of

the accurate mass (Gross, 1994). A key point to minimize error in accurate mass
measurement is ensuring that the target ion is completely free of interfering ions,
because these ions shift the mass of the target peak.
In general, high mass resolution and high mass accuracy depend on each other,
because the latter tends to improve as the former is improved. HR allows to separate
neighboring ions, and accurate mass can deliver molecular formulas (Gross, 2011).
Therefore, it is important to note that HR alone does not equally imply measuring
the accurate mass.

1.4 MASS CALIBRATION IN HIGH-RESOLUTION MASS

SPECTROMETRY
Mass calibration is a relevant process in every mass spectrometer for a proper rep-
resentation of ions in the m/z axis. It also results in a very important fact in HRMS
where not only high mass resolution but also high mass accuracy is critical (Gross,
2011). For that, typically, mass reference compounds with a compilation of well-
known m/z values are needed (Busch, 2004, 2005).
Calibration is frequently performed in an automatic or semiautomatic way by the
mass spectrometer software when the list of ions of those mass calibration com-
pounds are correlated with experimentally obtained m/z values. It is called external
mass calibration if the mass calibration is stored in a calibration file for further mea-
surements and the mass calibration standard is not used during acquisition of exper-
imental mass spectra. Frequency of recalibration has influence on mass accuracy of
the mass analyzer. The selection of the mass calibration compound depends on the
ionization method and, of course, the mass analyzer used. However, (1) they should
yield sufficient regularly spaced abundant ions across the entire scan range; (2) the
reference ions should have negative mass defects to prevent overlap with typical
compounds containing C, H, N, and O; and (3) they should be readily available,
chemically inert, and sufficiently volatile. Some of the most common calibration
standards and their masses and relative abundances can be found in literature
(Dass, 2007). For example, perfluorokerosene (PFK) is often established as a
mass calibration standard in electron ionization (EI). PFK provides numerous frag-
ment ions that may be used up to m/z 700e1100 depending on the type of mixture
used (commercially available from low to high boiling grades). Also, perflourotribu-
tylamine (FC-43) is also proposed as mass calibration standard thanks to its charac-
teristics ions up to 614 in an EI spectrum (Sack, Lapp, Gross, & Kimble, 1984).
When a high-mass calibration (i.e., up to 3000 u) is required, triazines and a mixture
of fluorinated phosphazenes called Ultramark can be used as reference calibrants.
For electrospray instruments, the most typical calibration standards are CsI, poly(-
ethylene glycol) (PEG), poly(ethylene glycol) bis(carboxymethyl ether), poly(eth-
ylene glycol monomethyl ether), and poly(propylene glycol). MALDI users also
have several reference compounds available, such as a-CHCA matrix (dimer þ Hþ),
10 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

4-hydroxy-3-methoxycinnamic acid (trimer þ Naþ), angiotensin I and II, bradyki-

nin, substance P, desArg1-bradykinin, gramicidin, and autodigestion products of
trypsin.
As an alternative, internal mass calibration can be performed. For that, the mass
calibration standard is introduced using a second inlet system into the ion source, for
instance, as a volatile standard. As an alternative, it can be mixed with the analyte
before analysis. This last option presents more limitations than the use of alternative
inlet systems.
Typical mass accuracy obtained by internal mass calibration used to be better
than those obtained by external calibration. Some examples are 0.1e0.5 ppm
with FT-ICR, 0.5e1 ppm with Orbitrap, 0.5e5 ppm with magnetic sector, or
1e10 ppm with TOF analyzers.
Fast atom bombardment instruments are sometimes internally calibrated with
good mass accuracy by using the matrix peaks for a mass calibration but it is
preferred a mixture of the standard with the analyte (matrix) if unwanted reactions
are not observed and proper solubility of the analyte and standard. One typical mass
calibration standard used is PEG with an average molecular weight of 600 u (PEG
600). In this sense, the reproducibility of mass calibration after several scan cycles is
improved because of affection of magnets by hysteresis.
MALDI mass calibration can be compromised if thick sample layers are used
with on-axis TOF instruments. However, orthogonal acceleration TOF analyzers
present better results. In some cases, for example, in the analysis of synthetic poly-
mers, the formation of evenly spaced oligomer ions can be used as internal mass
calibration (Dienes et al., 1996). In the case of TOF analyzers, the conversion
from a measured flight time to mass requires a mass calibration. The computer
makes the calculations using proper algorithms once the values of flight time for
a few calibrant masses are known. Sometimes, a second calibration step is requested
to achieve enough accuracy (Ferrer & Thurman, 2009). It must be carefully
controlled changes in flight distances or accelerating potentials to obtain mass accu-
racies of 1 ppm, but again, the internal mass calibration can correct such instrument
factors with an automatic data processing carried out at the same time as that of the
analysis of the sample. Generally, a mass calibration per day or week is enough to
obtain a proper accuracy of m/z for many TOF instruments, but it is adequate to use
internal mass calibration, especially when long analyses are performed (Chernush-
evich, Loboda, & Thomson, 2001).
FT-ICR mass analyzers with superconducting magnets are frequently very stable
for many days of use in normal applications. In this case, a mass accuracy better than
1 ppm can be achieved in a wide mass range (Rodgers, Blumer, Hendrickson, &
Marshall, 2000).
Some HR mass spectrometers such as double focusing systems (DFS) can be
operated by multiple ion detection (MID) mode where the intensities of some
ions typical of a target analyte can be continuously monitored to increase sensitivity,
precision, and selectivity of the method. A monitoring window is selected if the
 1.4 Mass Calibration in High-Resolution Mass Spectrometry 11

instrument is coupled to a chromatographic inlet device (gas or liquid chromato-

graph). For data acquisition, the magnet gets blocked in one mass and electric scans
are carried out modifying the acceleration voltage. Each scan suffers a rectification
of the mass calibration at the same time that experimental data are obtained. This
technique is called lock-mass technique and improves mass accuracy increasing reli-
ability of mass spectrometric data obtained. Resolution of the instrument can also be
recalculated on each scan. It can also be improved doubling the calibration masses in
a technique called Lock-plus-cali mass technique. This scan-to-scan mass calibra-
tion processed in the background improves confidence of the analytical data. For
this internal mass calibration, the calibration standard is leaked continuously from
the reference inlet system into the ion source. Two ion masses are selected from
the reference substance: one mass that is below the analyte target masses and another
one above the analyte target masses. The lowest mass is called “lock mass” and the
highest is named “calibration mass.” The magnet is locking the magnet at the start of
each MID process and performing a mass calibration based on the lock mass. All
analyzer jumps to the calibration and target masses by fast electrical jumps of the
acceleration voltage. It provides a fine calibration in only a very few milliseconds
(Thermo Fisher Scientific Inc., 2007). Fig. 1.3 shows the typical sequence of steps
during a MID process in DFS instrument.

FIGURE 1.3
Internal mass calibration and target mass detection during a multiple ion detection (MID)
process in a double focusing system (DFS) instrument: A, magnet locking and lock mass
sweep. Mass calibration and resolution determination; B, electrical jump to calibration
mass; C, calibration mass sweep and mass calibration; D, electrical jumps to target
masses; E, electrical jump to calibration mass for mass calibration.
12 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

1.5 GENERAL CONSIDERATIONS

Empirical determination of a molecular formula for a substance can be very useful in
organic MS. HRMS can be an alternative to traditional chemical methods based on
the tedious, slow, and often inaccurate process of breaking down of a known weight
of a molecule into its constituent elements and weight of them (Herbert & Johstone,
2003). It should be mentioned that the mass of an electron is very small compared
with masses of any element, and therefore, frequently, the mass of Mþ is considered
the same as that of M. Therefore, an HR mass spectrometer can be used to measure
relative atomic, molecular, or fragment ion masses with high accuracy. An accept-
able value of the measured mass should be within 5 ppm of the accurate mass (Gross,
1994).
It is essential that the ion of interest is properly resolved from all other neigh-
boring ions because any interfering ion would introduce an error in mass measure-
ment. Therefore, a high resolving power is very important for accurate mass
measurements. For small molecules, a resolving power higher than, i.e., 10,000 is
not critical. For example, a resolving power of 770 would be enough for mass-
resolving C2 H4 þ (28.031300) and COþ (27.994915). Nevertheless, a resolving po-
 

wer of at least 5500 is needed to separate C13 H16 eC2 H4 þ and C13 H16 eCOþ ions,
 

even if the difference between both masses is 0.036385 u. Another difficulty is that
the possible elemental composition becomes quite larger as the mass increases.
Full scan can be one of the simplest acquisition modes to obtain an accurate mass
value when an internal mass calibration is carried out. Accurate masses of all ions
can be determined in one single chromatographic run, and elemental composition
can be achieved with an adequate accuracy of less than 5 ppm. Peak-matching
mode is a more accurate mass measurement technique with a typical accuracy lower
than 0.3 ppm. For that, only one ion is determined at a time, for example, using the
MID technique described earlier. It is recommended that the mass of the mass cali-
bration ion must be within 2% of the unknown mass to give the highest accuracy. A
combination of slow scanning of the accelerating voltage and computer programs
that improve signal averaging, smoothing, and peak centroiding improves mass ac-
curacy (Hammar, Pettersson, & Carpenter, 1974).
A nominal mass may result from several combinations of elements, but only one
composition can match an accurate mass. Nevertheless, more possible combinations
can occur with an increased number of atoms in a molecule. A list of potential mo-
lecular formulas for various masses has been proposed (Beynon & Williams, 1963).
Diverse algorithms and computer programs are available for elemental composition;
many of them are available online.
Finally, it should be mentioned that RDm is also a valuable tool for confirmation
purposes. The sum of RDm of all isotopes of the molecule is defined as the isotopic
mass average (IMA), and Padilla-Sánchez et al. (2012) used this approach for the
reliable identification of small pesticides such as ethephon and N-acetyl-glufosinate,
obtaining an experimental IMA(Aþ2) value of 0.00286 Da for ethephon, which was
within the theoretical interval of 0.0029  0.0001 Da.
 References 13

ACKNOWLEDGMENTS
The authors gratefully acknowledge Andalusian Regional Government (Regional Ministry of
Innovation, Science, and Enterprise) and FEDER for financial support (Project Ref. P-12-
FQM 1838).

REFERENCES
Beynon, J. H., & Williams, A. E. (1963). Mass and abundance tables for use in mass
spectrometry. Amsterdam: Elsevier.
Bristow, A. W. T., & Webb, K. S. (2003). Intercomparison study on accurate mass measure-
ment of small molecules in mass spectrometry. Journal of the American Society for Mass
Spectrometry, 14(10), 1086e1098.
Busch, K. L. (2004). Masses in mass spectrometry: Balancing the analytical scales.
Spectroscopy, 19(11), 32e34.
Busch, K. L. (2005). Masses in mass spectrometry: Perfluors and more. Part II. Spectroscopy,
20(2), 76e81.
Chernushevich, I. V., Loboda, A. V., & Thomson, B. A. (2001). An introduction to
quadrupole-time-of-flight mass spectrometry. Journal of Mass Spectrometry, 36(8),
849e865.
Dass, C. (2007). Fundamentals of contemporary mass spectrometry. Hoboken, New Jersey:
John Wiley & Sons, Inc.
Dienes, T., Salvador, J. P., Schürch, S., Scott, J. R., Yao, J., Cui, S., et al. (1996). Fourier trans-
form mass spectrometrydadvancing years (1992-mid. 1996). Mass Spectrometry Re-
views, 15(3), 163e211.
Ekman, R., Silberring, J., Westman-Brinkmalm, A., & Kraj, A. (Eds.). (2009). Mass spectrom-
etry. Instrumentation, interpretation, and applications. Hoboken, New Jersey: John Wiley
& Sons, Inc.
Ferrer, I., & Thurman, E. M. (2009). Liquid chromatography time-of-flight mass spectrometry e
principles, tools, and applications for accurate mass analysis. Hoboken: Wiley-
Interscience.
Gross, J. H. (2011). Mass spectrometry. A textbook (2nd ed.). Berlin Heidelberg: Springer.
Gross, M. L. (1994). Accurate masses for structure confirmation. Journal of the American So-
ciety for Mass Spectrometry, 5(2), 57.
Hammar, C. G., Pettersson, G., & Carpenter, P. T. (1974). Computerized mass fragmentogra-
phy and peak matching. Biomedical Mass Spectrometry, (1), 397e411.
Herbert, C. G., & Johstone, R. A. W. (2003). Mass spectrometry basics. Boca Ratón: CRC
Press.
de Hoffmann, E., & Stroobant, V. (2007). Mass spectrometry. Principles and applications (3rd
ed.). Chichester: John Wiley & Sons Ltd.
IUPAC. Compendium of chemical Terminology, 2nd ed. (the “Gold Book”). Compiled by A.
D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML
on-line corrected version: http://goldbook.iupac.org (2006) created by M. Nic, J. Jirat, B.
Kosata; updates compiled by A. Jenkins.
Kim, S., Rodgers, R. P., & Marshall, A. G. (2006). Truly “exact” mass: elemental composition
can be determined uniquely from molecular mass measurement at w0.1 mDa accuracy
14 CHAPTER 1 HRMS: Fundamentals and Basic Concepts

for molecules up to w500 Da. International Journal of Mass Spectrometry, 251(2e3),

260e265.
Lin, L., Lin, H., Zhang, M., Dong, X., Yin, X., Qub, C., et al. (2015). Types, principle, and
characteristics of tandem high-resolution mass spectrometry and its applications. RSC Ad-
vances, 5, 107623e107636. Royal Society of Chemistry.
Marshall, A. G., Hendrickson, C. L., & Shi, S. D. H. (2002). Scaling MS plateaus with high-
resolution FT-ICRMS. Analytical Chemistry, 74(9), 252Ae259A.
Mcluckey, S. A., & Wells, J. M. (2001). Mass analysis at the advent of the 21st century.
Chemical Reviews, 101(2), 571e606.
Murray, K. K., Boyd, R. K., Eberlin, M. N., Langley, G. J., Li, L., & Naito, Y. (2013). Def-
initions of terms relating to mass spectrometry (IUPAC Recommendations 2013). Pure
and Applied Chemistry, 85(7), 1515e1609.
Padilla-Sánchez, J. A., Plaza-Bolaños, P., Romero-González, R., Grande-Martı́nez, A.,
Thurman, E. M., & Garrido-Frenich, A. (2012). Innovative determination of polar organo-
phosphonate pesticides based on high-resolution Orbitrap mass spectrometry. Journal of
Mass Spectrometry, 47, 1458e1465.
Picó, Y. (2015). Advanced mass spectrometry. In Y. Picó (Ed.), Comprehensive analytical
chemistry (Vol. 68). Amsterdam: Elsevier.
Price, P. (1991). Standard definitions of terms relating to mass spectrometry. A report from
the committee on measurements and standards of the American Society for
Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 2(4),
336e348.
Rodgers, R. P., Blumer, E. N., Hendrickson, C. L., & Marshall, A. G. (2000). Stable isotope
incorporation triples the upper mass limit for determination of elemental composition by
accurate mass measurement. Journal of the American Society for Mass Spectrometry,
11(10), 835e840.
Sack, T. M., Lapp, R. L., Gross, M. L., & Kimble, B. J. (1984). A method for the statistical
evaluation of accurate mass measurement quality. International Journal of Mass Spec-
trometry and Ion Processes, 61(2), 191e213.
Sparkman, O. D. (2006). Mass spec desk reference (2nd ed.). Pittsburgh: Global View
Publishing.
Thermo Fisher Scientific Inc.. (2007). [Online], Available from http://tools.thermofisher.com/
content/sfs/brochures/high-resolution-mid-data-acquisition-for-target-compound-
analysis-with-the-dfs-gcms-system.pdf.
Thurman, E. M., & Ferrer, I. (2010). The isotopic mass defect: A tool for limiting molecular
formulas by accurate mass. Analytical and Bioanalytical Chemistry, 397, 2807e2816.
Xian, F., Hendrickson, C. L., & Marshall, A. G. (2012). High resolution mass spectrometry.
Analytical Chemistry, 84, 708e719.