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INTRODUCTION
The basic steps of mass spectrometry (MS) begin with sample preparation, ionization,
mass filtering, and detection. MS quantifies and identifies the species molar mass and
the molar mass of fragments. High resolution mass spectrometry discriminates between
and identifies the chemical formulas of molecules with
Description
Mass spectrometers first ionize target molecules into radical cations with
an odd number of electrons (Figure 1).[8] Molecules and fragments then pass
through a mass filter in which a magnetic or electric field deflects their trajectory
in proportion to the mass-to-charge ratio (m/Z): heavier ions deflect less and
highly charged ions deflect more. At the exit of the mass filter, ions are detected
in proportion to their relative abundance. We arbitrarily assign a value of
100 % to the most intense peak (base peak) and values of the other peaks are
in proportion to their intensity with respect to the base peak (Figure 2).
Ion Sources
Electron ionization (EI) was the first technique applied to fragment molecules
in the gas phase at high vacuum (0.001 Pa).[9] A heated filament generates elec-
trons that accelerate towards an anode and impact and ionize neutral atoms
in their path. Methane, for example, takes a positive charge and produces a
second electron:
CH4 + 1e− →
− CH+
4 + 2e
−
(1)
We refer to this process as hard ionization as the electrons often fragment the
molecules. EI fragments molecules in proportion to the applied energy (ioniza-
tion voltage).
Soft ionization techniques produce fewer fragments because the ions have less
excess energy. Chemical ionization (CI) was the first soft ionization technique,
followed by fast atom bombardment (FAB), then its parent liquid secondary ion-
ization (LSI), and matrix-assisted laser desorption ionization (MALDI), among
others.[10, 4] . Biomolecular chemistry applies CI: a reagent protonates the target
in the gas phase under weak vacuum at low temperature to minimize thermal
degradation. The ions generated collide producing strong acids (NH4+ from
M+
M+
Electron ionisation M+
M+
M’+
RF signal current
ion trap
sample (anode) ion extraction measurement
and focussing
M e-
e-
M
M+
Time-of-flight Electron multiplier
M M+
e - conversion
e-
e -
acceleration field-free drift dynode
anode
M+
pumping e-
paths
filament
(cathode)
heavy light
ions ions
current
measurement
E
field
Figure 1: Mass spectrometry components. Quadrupole and time-of-flight are the most com-
mon mass filters. MS manufactures may integrate both Faraday cup and electron multiplier
detectors.
Figure 2: Furfural fragmentation pattern. The measured spectra is in blue while the reference
spectra is in red. We assign the base peak 100 %.
Mass Filters
Mass analyzers separate ions on based on their mass-to-charge (m/Z) ra-
tio with static or dynamic electric and/or magnetic fields. Scanning analyzers
measure m/Z ratios sequentially, while simultaneous analyzers measures them
all at once. Performance parameters include:
• mass range (m/Z);
• acquisition frequency (mass scans per unit time);
• transmission efficiency of ions reaching the detector;
• mass accuracy (difference between theory and measurement);
• resolution (capability to discriminate ions with close m/Z values); and
• sensitivity, (C µg−1 ).[4]
The quadrupole mass filter belongs to the scanning family of analyzers along
with magnetic sector instruments. Quadrupole mass analyzers (QMA) are the
least expensive and easiest to operate but have relatively low resolution. They
consist of 4 circular or hyperbolic parallel rods and separate based on the ion
trajectory stability in the space between the rods. A high frequency alternat-
ing current superimposed on a direct voltage between pairs of opposing rods
generates a dynamic electric field. In a transmission QMA filter, we chose the
field frequency to allow only ions with a narrow m/Z ratio to pass through. All
other ions have unstable trajectories and lose their charge when they eventually
Detectors
Detectors generate an electrical current from the incoming ions proportion-
ately to their abundance. Point detectors count ions at a fixed location in space
either sending only a narrow m/Z range to this point (QMA) or segregating
the arriving ions in time (TOF). Array detectors count multiple m/Z ratios
simultaneously over a specific region where the mass analyzer segregates ions in
space (magnetic sector mass analyzers).
The Faraday cup is a simple point detector consisting of a metallic cup with
a small orifice open to the vacuum of the mass analyzer on the other side. It
generates a direct current when the grounded cup surface neutralizes the ion
beam. Accuracy is a function of how effective the cup prevents ion reflection
and secondary electron ejection. Cup geometry, coating, and the magnetic field
are design parameters to minimize these phenomena. Faraday cups are less
sensitive than other detectors and are best for abundant analytes. The lower
limit ranges from 50–100 ppm (1 µg g−1 ) depending on the electronics. Other
detectors can identify concentrations as low as a couple 1 ng g−1 .
Ions colliding with the surface of SEM detectors (secondary electron emis-
sion) generate secondary electrons and from the cascade effect, these electrons
also produce secondary electrons. Discrete dynodes at decreasing negative po-
tential and continuous dynodes (channeltron) with a voltage applied at the two
extremities amplify the current. The low frequency collision ions hitting the
detector surface generate a current that is amplified. SEMs scan more rapidly
than Farady detectors but are less precise. They are best suited for light ions
that generate more secondary ions due to their high speed compared to heavy
ions. Sputtering of the semiconductor-coated surface and contaminants limit
their lifetime to 1–2 y.
Figure 3: Relative sensitivity of binary mixture of light gases in Ar measured over a period of
one month with a Hiden QIC-20 quadrupole MS.
Calibration
Instrument sensitivity depends on ionization technique, mass filtering and
detection, vacuum chamber pressure, analyte molar mass, concentration, and
on the nature of the other constituents (space charge effect). The signal varies
linearly over +− two decades. Calibrating n species requires an n − 1 sen-
sitivity hyper-surface and mixtures of 3–5 gases require hundreds of reference
mixtures.[12] For example, when the concentration of an easy-to-ionize molecule
increases in the sample, the space charge density increases in the ionization
chamber and mass filter, which decreases sensitivity of the other species. Con-
sider the sensitivity of binary mixtures of small gaseous molecules diluted with
argon (Figure 3). When we replace argon with CO2 or CH4 , which have a
larger ionization cross section, sensitivity decreases asymptotically. Sensitiv-
ity increases when replacing Ar with He and H2 , which are more difficult to
ionize.[12]
We measured the relative sensitivities (RS) during a one month period.
The carbon dioxide relative sensitivity RS was the most accurate. Increasing
the concentration of each species reduces the RS of CH4 and CO2 most.
When the ionization cross-section of the manufacturer’s reference species is
known, relative sensitivity for other species is based on their cross-sections and
scales with the raw mass spectra with species-specific factors. When instruments
express m/Z peak intensity as partial pressure, the real signal intensity is the
ratio of measured intensity (Pmeas,i ) and relative sensitivity (RSi ).[13] The mole
fraction is then:
Pmeas,i
yi = P (3)
RSi i Pmeas,i
This approach accounts for ionization under idealized conditions but ignores
CO2 + 1e− →
− CO2+ +2e− (4)
CO + O+
CO2+
CO+ + O
Applications
The Web of Science Core Collection (WoS) indexed over 60 000 documents
in 2016 and 2017 that contained ”Mass Spectrometry” in the basic search tab,
which ranks it second after x-ray diffraction as the most frequently cited tech-
nique. A bibliometric map of the top 10 000 cited articles with mass spectrome-
try among the keywords identifies four research clusters (Figure 4). The small-
est cluster relates to water analysis, pharmaceuticals, and toxicity (blue circles
on the lower right). The next smallest field relates to several MS techniques
including tandem-MS, LC-MS, and urine analysis (beige circles on the lower
UNCERTAINTY
Limitations
The three components of a mass spectrometer are the ion source, mass filter,
and detector. We choose the ion source based on analyte composition and
biological
crystal structure
biosynthesis oxidation
milk
9
acid
gene expression
antibiotics
inflammation
risk assessment
diagnosis bisphenol a
exposure
serum
Figure 4: MS bibliometric map.[1, 24] The size of the keyword is proportional to the number of occurrences (from 87 to 1167—Tandem MS). The
distance between keywords shows how closely topics are related. The map includes the top 100 topics.
Accept e d Article
Figure 5: MS continuous monitoring of the effluent gas from a fluidized bed reactor—
dehydration of fructose to 5-hydroxymethyl furfural.[27] The gas composition of the feed at
t = 0 was 99.9 % (molar) Ar and 0.1 % O2 . At t = 10 min, a pump sparged a fructose-in-water
solution to the reactor. Consequently, the O2 signal dropped and the CO and CO2 signals
increased. Air leaks through fittings between the capillary and process lines so nitrogen con-
tributes to the 28 amu baseline signal, which we label as CO. During the 3 h experiment, we
sampled the quench immediately upstream of the MS take-off, which perturbs the system and
the signal: at 140 min, the oxygen signal increases simultaneously with the 28 amu, which
represents a large infiltration of air. The Ar signal drifts down from 5.8 × 10−8 at 0.5 h to
5.0 × 10−8 at 3 h. Coincidentally, the O2 signal drops from 4.8 × 10−11 to 3.4 × 10−11 .
10
Sources of Error
Contrary to many other analytical instruments, mass spectrometry reports
quantitative data terms of the molar mass of the consituents and their relative
abundance. When we want to identify the presence of an analyte in a sample,
the main error relates to assessing its mass—its resolving power. Errors with a
QMS are on the order of 0.1–0.5 amu (<0.1 %), while mass accuracy of other
mass filtering approaches are 3 orders of magnitude better (<0.002 %).
Calibration is necessary to quantify (rather than identify) mixture composi-
tions, which entails relating ionic current at the detector to the relative abun-
dance of all constituents. The intrinsic non-linearity of the ion source and mass
11
Detection Limits
The minimum amount or proportion of a substance that MS detects or quan-
tifies depends on its mass. Detection limits depend on the efficiencies to ionize,
filter, and detect a specific mass. Only high-resolution (HRMS) or tandem (MS-
MS) mass spectrometry report non-zero signals, so defining an instrument de-
tection requires identifying a signal sufficiently different from background noise
to be quantifiable.
When an MS samples a gas stream continuously, we define detection limits
in terms of the relative abundance of a constituent. EI-QMS instruments with
electron mulitplier detectors have gas phase detection limits of of 100 ppb. More
sophisticated QMS can achieve detection limits of a few ppb.
For GC-MS or LC-MS, an MS measures each peak of the analytes that
elute from the column. Detection limit expressed in terms of concentration is
of little interest since the injection volume and the flow rate of carrier fluid
varies between instruments. Rather we express detection limit in terms of the
minimum mass of a substance that must be present in the sample introduced
in the column. When coupled with adapted detectors, the mass filters detect
analytes from the pg to fg range (Table 1). Increasing the scan rate increases
the detection limit because there is less time to measure a signal for each specific
m/Z ratio. For this reason, the TOF high scanning rates have higher (poorer)
detection limits compared with other mass filters.
CONCLUSIONS
12
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