Mass Spectrometry : Mass Spectrometry Powerful analytical technique Smallest scale

Destructive technique Useful for identification of species According to the IUPAC (International
Union of Pure and Applied Chemistry), it is the branch of science dealing with all aspects of
mass spectroscopes and results obtained with these instruments.
Mass Spectrometry : Mass Spectrometry Brief History of Mass Spectrometry Nobel prize
pioneers Mass spectrometer Contents Structural analysis and Fragmentation Patterns
interpretation of mass spectrum Applications of mass spectrometry
Mass Spectrometry : Mass Spectrometry J.J. Thomson. Discovered electrons by cathode rays
experiment. Nobel prize in 1906. Francis Aston recognized 1st mass spectrometer and
measure z/m of ionic compounds. First double focusing magnetic analyzer was invented by
Johnson and Neil. Munson and Field described chemical ionization. Brief History of Mass
Spectrometry
Mass Spectrometry : Mass Spectrometry Electrospray Ionization was invented by Dole, Mack
and friends. Atmospheric Pressure Chemical Ionization (APCI) was developed by Carroll and
others. F. Hillenkamp, M.Karas and co-workers describe and coin the term matrix assisted laser
desorption ionization (MALDI). w. Paul discovered the ion trap technique.
Mass Spectrometry : Mass Spectrometry Nobel prize pioneers
Mass Spectrometry : Mass Spectrometry Mass spectrometer
Mass Spectrometry : Mass Spectrometry Understanding Mass Spectrometry In a mass
spectrometer, the same thing is happening, except it's atoms and molecules that are being
deflected, and it's electric or magnetic fields causing the deflection. It's also happening in a
cabinet that can be as small as a microwave or as large as a chest freezer.
Mass Spectrometry : Mass Spectrometry Mass spectrometer is similar to a prism. In the
prism, light is separated into its component wavelengths which are then detected with an
optical receptor, such as visualization. Similarly, in a mass spectrometer the generated ions
are separated in the mass analyzer, digitized and detected by an ion detector.
Mass Spectrometry : Mass Spectrometry Basic Components of Mass Spectrometer Four
basic components Sample inlet Ionization source Mass analyzer Ion detector
Mass spectrometer : Mass spectrometer Sample Introduction Techniques Initial pressure of
sample is 760 mmHg or ~10-6 torr Direct Insertion (commonly used in MALDI) Direct infusion
or injection (commonly used in ESI) Two techniques
Mass spectrometer : Mass spectrometer Direct Insertion sample introduction technique very
simple technique Sample is placed on a prob and inserted into ionization source and then
subjected to any number of desorption processes, such as laser desorption or direct heating, to
facilitate vaporization and ionization.
Mass Spectrometry : Mass Spectrometry Direct infusion or injection sample introduction
technique Frequently used due to high efficiently Used in coupling techniques like GC-MS and
HPLC-MS
Mass Spectrometry : Mass Spectrometry Ionization Methods used in Mass spectrometry
Commonly used Protonation Deprotonation Cationization Transfer of a charged molecule to the
gas phase Electron ejection Electron capture
Mass Spectrometry : Mass Spectrometry Protonation Formation of positive ions by the
addition of a proton Used for basic compounds like amines, peptides Used in MALDI, APCI and
ESI
Mass Spectrometry : Mass Spectrometry Deprotonation Give net negative charge of 1- by
removal of one proton Used for acidic species like phenols, carboxylic acid, sulfonic acid etc.
Used in MALDI, APCI and ESI
Mass Spectrometry : Mass Spectrometry Cationization produces a charged complex by non-
covalently adding a positively charged ion like alkali metal ion or ammonium ion to a neutral
molecule. Used for Carbohydrates Used in MALDI, APCI and ESI
Mass Spectrometry : Mass Spectrometry Transfer of a charged molecule to the gas phase
Cation from solution to gas Used in MALDI or ESI
Mass Spectrometry : Mass Spectrometry Electron ejection Electron is ejected to give positive
ion Usually for non-polar compounds with low molecular weights like anthracene.
Mass Spectrometry : Mass Spectrometry Electron capture a net negative charge of 1- is
achieved with the absorption or capture of an electron. Used for halogenated compounds
Mass Spectrometry : Mass Spectrometry Ionization Sources in mass spectrometer
Electrospray Ionization (ESI) Nanoelectrospray Ionization (NanoESI) Atmospheric Pressure
Chemical Ionization (APCI) Atmospheric pressure photoionization (APPI) Matrix-assisted laser
desorption/ionization mass spectrometry (MALDI-MS) Fast Atom Bombardment (FAB) Electron
Ionization (EI) Chemical Ionization (CI) Thermal ionization (TI)
Mass Spectrometry : Mass Spectrometry Ionization Sources Hard ionization sources Soft
ionization sources leave excess energy in molecule and produced stable fragments which is
not further fragarmented Little excess energy in molecule and produced unstable fragments
which are again fragmented. Types of
Mass Spectrometry : Mass Spectrometry Electrospray Ionization (ESI) For example peptides,
proteins, carbohydrates, small oligonucleotides, synthetic polymers, and lipids The sample
solution is sprayed from a region of the strong electric field at the tip of a metal nozzle
maintained at a potential of anywhere from 700 V to 5000 V. The nozzle (or needle) to which
the potential is applied serves to disperse the solution into a fine spray of charged droplets.
Either dry gas, heat, or both are applied to the droplets at atmospheric pressure thus causing
the solvent to evaporate from each droplet
Mass Spectrometry : Mass Spectrometry Nanoelectrospray Ionization (NanoESI) where the
spray needle has been made very small and is positioned close to the entrance to the mass
analyzer. The end result of this rather simple adjustment is increased efficiency, which
includes a reduction in the amount of sample needed. Very sensitive very low flow rates Very
small droplet size (~5µ)
Mass Spectrometry : Mass Spectrometry Atmospheric Pressure Chemical Ionization (APCI)
the liquid effluent of APCI is introduced directly into the ionization source. However, the
similarity stops there. The droplets are not charged and the APCI source contains a heated
vaporizer, which facilitates rapid desolvation/vaporization of the droplets. Vaporized sample
molecules are carried through an ion-molecule reaction region at atmospheric pressure.
Mass Spectrometry : Mass Spectrometry Atmospheric pressure photoionization (APPI) it
generates ions directly from solution with relatively low background and is capable of
analyzing relatively nonpolar compounds. APPI vaporized sample passes through ultra-violet
light. APPI is much more sensitive than ESI or APCI.
Mass Spectrometry : Mass Spectrometry Matrix-assisted laser desorption/ionization mass
spectrometry (MALDI-MS) the analyte is first co-crystallized with a large molar excess of a
matrix compound, usually a UV-absorbing weak organic acid. Irradiation of this analyte-matrix
mixture by a laser results in the vaporization of the matrix, which carries the analyte with it.
The matrix plays a key role in this technique. The co-crystallized sample molecules also
vaporize, but without having to directly absorb energy from the laser. Molecules sensitive to
the laser light are therefore protected from direct UV laser excitation.
Mass Spectrometry : Mass Spectrometry Fast Atom Bombardment (FAB) Immobilized matrix
is bombarded with a fast beam of Argon or Xenon atoms. Charged sample ions are ejected
from the matrix and extracted into the mass analyzers Used for large compounds with low
volatility (eg peptides, proteins, carbohydrates) Solid or liquid sample is mixed with a non-
volatile matrix (eg glycerol, crown ethers, nitrobenzyl alcohol)
Mass Spectrometry : Mass Spectrometry Electron Ionization (EI) Energetic process a heated
filament emits electrons which are accelerated by a potential difference of usually 70eV into
the sample chamber. Ionization of the sample occurs by removal of an electron from the
molecule thus generating a positively charged ion with one unpaired electron. Produces
M+.radical cation giving molecular weight Produces abundant fragment ions
Mass Spectrometry : Mass Spectrometry Chemical Ionization (CI) process is initiated with a
reagent gas such as methane, isobutane, or ammonia, which is ionized by electron impact.
High gas pressure in the ionization source is required for the reaction between the reagent gas
ions and reagent gas neutrals. possible mechanism Reagent (R) + e- → R+ + 2 e- R+ + RH →
RH+ + R RH+ + Analyte (A) → AH+ + R biologically important molecules (sugars, amino acids,
lipids etc.).
Mass Spectrometry : Mass Spectrometry Thermal ionization (TI) Samples are deposited on
rhenium or tantalum filament and then carefully evaporated and sent to mass analyzer. used
to quantify toxic trace elements in foods. measurement of stable isotope ratio of inorganic
elements.
Mass Spectrometry : Mass Spectrometry Accuracy The range over which a mass
spectrometer analyzer can operate. A measure of how well a mass spectrometer separates
ions of different mass is a measure of how close the value obtained is to the true value. The
accuracy varies dramatically from analyzer to analyzer depending on the analyzer type and
resolution. Mass Range Resolution Scan Speed Mass Analyzer Properties of mass Analyzer
Analyzers are scanned with a regular cycle time from low to high m/z or vice versa.
Mass Spectrometry : Mass Spectrometry Mass Analyzer Quadrupoles Quadrupole Ion Trap
Linear Ion Trap Double-Focusing Magnetic Sector Quadrupole Time-of-Flight Tandem MS
Quadrupole Time-of-Flight MS
Mass Spectrometry : Mass Spectrometry Quadrupoles -ions travel parallel to four rods -
opposite pairs of rods have rapidly alternating potentials (AC) - ions try to follow alternating
field in helical trajectories - stable path only for one m/z value for each field frequency Smalll
and low cost Rmax ~ 500 Harder to push heavy molecule - m/zmax < 2000
Mass Spectrometry : Mass Spectrometry Quadrupole Ion Trap The quadrupole ion trap
typically consists of a ring electrode and two hyperbolic endcap electrodes. The motion of the
ions induced by the electric field on these electrodes allows ions to be trapped or ejected from
the ion trap. In the normal mode, the radio frequency is scanned to resonantly excite and
therefore eject ions through small holes in the endcap to a detector. As the RF is scanned to
higher frequencies, higher m/z ions are excited, ejected, and detected.
Mass Spectrometry : Mass Spectrometry Linear Ion Trap The linear ion trap differs from the
3D ion trap as it confines ions along the axis of a quadrupole mass analyzer using a two-
dimensional (2D) radio frequency (RF) field with potentials applied to end electrodes. The
primary advantage to the linear trap over the 3D trap is the larger analyzer volume lends itself
to a greater dynamic ranges and an improved range of quantitative analysis.
Mass Spectrometry : Mass Spectrometry Double-Focusing Magnetic Sector the ions are
accelerated into a magnetic field using an electric field. A charged particle traveling through a
magnetic field will travel in a circular motion with a radius that depends on the speed of the
ion, the magnetic field strength, and the ion’s m/z. A mass spectrum is obtained by scanning
the magnetic field and monitoring ions as they strike a fixed point detector.
Mass Spectrometry : Mass Spectrometry Quadrupole Time-of-Flight Tandem MS Time-of-
flight analysis is based on accelerating a group of ions to a detector where all of the ions are
given the same amount of energy through an accelerating potential. Because the ions have
the same energy, but a different mass, the lighter ions reach the detector first because of their
greater velocity, while the heavier ions take longer due to their heavier masses and lower
velocity. Hence, the analyzer is called time-of-flight because the mass is determined from the
ions’ time of arrival. Mass, charge, and kinetic energy of the ion all play a part in the arrival
time at the detector.
Mass Spectrometry : Mass Spectrometry Quadrupole Time-of-Flight MS Quadrupole-TOF
mass analyzers are typically coupled to electrospray ionization sources and more recently they
have been successfully coupled to MALDI. It has high efficiency, sensitivity, and accuracy as
compared to Quadrupole and TOF analyzer.
Mass Spectrometry : Mass Spectrometry Photomultiplier Conversion Dynode Faraday Cup
Array Detector Charge (or Inductive) Detector Electron Multiplier Detectors used in mass
spectrometer
Mass Spectrometry : Mass Spectrometry Faraday Cup A Faraday cup involves an ion striking
the dynode (BeO, GaP, or CsSb) surface which causes secondary electrons to be ejected. This
temporary electron emission induces a positive charge on the detector and therefore a current
of electrons flowing toward the detector. not particularly sensitive offering limited amplification
of signal is tolerant of relatively high pressure. – Ions are accelerated toward a grounded
“collector electrode” – As ions strike the surface, electrons flow to neutralize charge, producing
a small current that can be externally amplified. – Size of this current is related to # of ions in –
No internal gain → less sensitive
Mass Spectrometry : Mass Spectrometry Photomultiplier Conversion Dynode is not as
commonly Life limit is high as compared to others. the secondary electrons strike a
phosphorus screen instead of a dynode. The phosphorus screen releases photons which are
detected by the photomultiplier. Photomultipliers also operate like the electron multiplier
where the striking of the photon on scintillating surface results in the release of electrons that
are then amplified using the cascading principle.
Mass Spectrometry : Mass Spectrometry Array Detector detects ions according to their
different m/z, has been typically used on magnetic sector mass analyzers. The primary
advantage of this approach is that, over a small mass range, scanning is not necessary and
therefore sensitivity is improved.
Mass Spectrometry : Mass Spectrometry Charge (or Inductive) Detector Charge detectors
simply recognize a moving charged particle (an ion) through the induction of a current on the
plate as the ion moves past Detection is independent of ion size.
Mass spectrometer : Mass spectrometer Electron Multiplier Most important part made up of
a series (12 to 24) of aluminum oxide (Al2O3) dynodes Used for increasing potential Ions strike
the first dynode surface causing an emission of electrons. These electrons are then attracted
to the next dynode held at a higher potential and therefore more secondary electrons are
generated.
Mass spectrometer : Mass spectrometer Vacuum in the Mass Spectrometer All mass
spectrometers need a vacuum to allow ions to reach the detector without colliding with other
gaseous molecules or atoms. If such collisions did occur, the instrument would suffer from
reduced resolution and sensitivity.
Mass spectrometer : Mass spectrometer Structural analysis and Fragmentation Patterns
Molecular ion (Parent ion) Fragmentation peaks Base peak Isotopic peaks . Mass spectrum
Graph of ion intensity (relative abundance) along x-axis versus mass-to-charge ratio (m/z)
(units daltons, Da) along Y-axis
Mass spectrometer : Mass spectrometer Molecular ion (Parent ion) the peak corresponding
to the mol wt of the compound The peak of an ion formed from the original molecule by
electron ionization, by the loss of an electron, or by addition or removal of an anion or cation
and also known as parent peak, radical peak.
Mass spectrometer : Mass spectrometer Fragmentation peaks The peaks observed by
fragments of compounds. The molecular ions are energetically unstable, and some of them will
break up into smaller pieces. The simplest case is that a molecular ion breaks into two parts -
one of which is another positive ion, and the other is an uncharged free radical. The uncharged
free radical won't produce a line on the mass spectrum. Only charged particles will be
accelerated, deflected and detected by the mass spectrometer. These uncharged particles will
simply get lost in the machine - eventually, they get removed by the vacuum pump.
Mass Spectrometry : Mass Spectrometry Base peak The most intense (tallest) peak in a
mass spectrum, due to the most abundant ion. Not to be confused with molecular ion: base
peaks are not always molecular ion and molecular ion are not always base peaks.
Mass Spectrometry : Mass Spectrometry Fragmentation Patterns By using fragmentation
pattern we can easily study the structure of a compound. Stevenson’s Rule Homolytic bond
cleavage Heterolytic fragmentation Alpha cleavage Beta-cleavage Inductive cleavage Retro
Diels-Alder Cleavage McLafferty rearrangement Ortho effect Onimum Reaction CO Elimination
Mass Spectrometry : Mass Spectrometry Stevenson’s Rule The most probable fragmentation
is the one that leaves the positive charge on the fragment with the lowest ionization energy In
other words, fragmentation processes that lead to the formation of more stable ions are
favored over processes that lead to less-stable ions. Cleavages that lead to the formation of
more stable carbocations are favored. When the loss of more than one possible radical is
possible, a corollary to Stevenson’s Rule is that the largest alkyl radical to be lost
preferentially.
Mass Spectrometry : Mass Spectrometry Homolytic bond cleavage A type of ion
fragmentation in which a bond is broken by the transfer of one electron from the bond to the
charged atom, the other electron remaining on its starting atom. The movement of one
electron is signified by a fishhook arrow. The fragmentation of a ketone is shown in the figure.
Mass Spectrometry : Mass Spectrometry Heterolytic bond cleavage type of ion
fragmentation in which a bond is broken by the transfer of a pair of electrons from the bond to
the charged atom The movement of 2 electrons is signified by a double-barbed arrow and also
referred to as charge-induced fragmentation.
Mass Spectrometry : Mass Spectrometry Alpha cleavage For example in alcohols, aliphatic
ethers, aromatic ethers, cyclic compounds and aromatic ketones etc. Alpha cleavage occurs on
α-bonds adjacent to heteroatoms (N, O, and S). Charge is stabilized by heteroatom. Occurs
only once in a fragmentation (cation formed is too stable to fragment further)
Mass Spectrometry : Mass Spectrometry Beta-cleavage Fission of a bond two removed from
a heteroatom or functional group, producing a radical and an ion. Also written as β-cleavage.
For example allylic fragmentation.
Mass Spectrometry : Mass Spectrometry Inductive cleavage If an electron pair is completely
transferred towards a centre of positive charge as a result of the inductive effect, shown
schematically by the use of a double-headed arrow, then the ion will fragment by inductive
cleavage. The figure illustrates this for a radical cation ether.
Mass Spectrometry : Mass Spectrometry Retro Diels-Alder Cleavage A multicentered ion
fragmentation which is the reverse of the classical Diels-Alder reaction employed in organic
synthesis that forms a cyclic alkene by the cycloaddition of a substituted diene and a
conjugated diene. In the retro reaction, a cyclic alkene radical cation fragments to form either
a diene and an alkene radical cation or a diene radical cation and an alkene. Depending on the
substituents present in the original molecule, the more stable radical cation will dominate.
Mass Spectrometry : Mass Spectrometry McLafferty rearrangement An ion fragmentation
characterised by a rearrangement within a six-membered ring system. The most usual
configuration is for a radical cation formed by EI to undergo the transfer of a γ- hydrogen atom
to the ionisation site through a ring system as shown here. The distonic radical cation so
formed can break up by radical-site-induced (α), or charged site-induced fragmentation as
shown in the figure. For example ketones, carboxylic acid and esters.
Mass Spectrometry : Mass Spectrometry Ortho effect The interaction between substituents
oriented ortho, as opposed to para and meta, to each other on a ring system, can create
specific fragmentation pathways. This permits the distinction between these isomeric species.
The diagram shows a case in which only the ortho isomer can undergo the rearrangement.
Mass Spectrometry : Mass Spectrometry Onium Reaction Mostly observed in cationic
fragments containing a heteroatom as charge carrier, e.g. oxonium, ammonium, phosphonium
and sulphonium ions. The onium reaction is not limited to alkyl substituents acyl groups can
also undergo the onium reaction Onium Ion: A hypervalent species containing a non-metallic
element such as the methonium ion CH5+. It includes ions such as oxonium, phosphonium,
and nitronium ions.
Mass Spectrometry : Mass Spectrometry CO Elimination If there is more than one CO group
present sequential elimination of all CO groups is possible. From carbonyl compounds CO
elimination reaction takes place like in aldehyde, ketones and phenols etc Cyclic unsaturated
carbonyl compounds and cationic carbonyl fragments which resulted from an a-cleavage tend
to eliminate CO .
Mass Spectrometry : Mass Spectrometry Rules for interpretation of mass spectrum DBR
Calculations Nitrogen Rule Isotopic effect
Mass Spectrometry : Mass Spectrometry Double bond or ring calculations tell us about how
many rings or double bonds are present in a compound. DBR= C-H/2+N/2+1 C= number of
carbon atoms H= number of hydrogen atoms N= number of nitogen atoms DBR Calculations
Mass Spectrometry : Mass Spectrometry Nitrogen Rule If a compound contains an even
number of nitrogen atoms (or no nitrogen atoms), its molecular ion will appear at an even
mass number. • If, however, a compound contains an odd number of nitrogen atoms, then its
molecular ion will appear at an odd mass value. • This rule is very useful for determining the
nitrogen content of an unknown compound.
Mass Spectrometry : Mass Spectrometry Isotopic effect
Mass Spectrometry : Mass Spectrometry Mass spectra (examples) Alkanes Strong M+ (but
intensity decreases with an increase of branches. Carbon-carbon bond cleavage loss of CH
units in series: M-14, M-28, M-42 etc
Mass Spectrometry : Mass Spectrometry Alkanes
Mass Spectrometry : Mass Spectrometry Cycloalkanes Strong M+, strong base peak at M-28
(loss of ethene) A series of peaks: M-15, M-28, M-43 etc Methyl, ethyl, propyl with an additional
hydrogen give peaks
Mass Spectrometry : Mass Spectrometry Alkenes Strong M+ Fragmentation ion has formula
CnH2n+ and CnH2n-1 -Cleavage A series of peaks: M-15, M-29, M-43, M-57 etc
Mass Spectrometry : Mass Spectrometry Alkynes Strong M+ Strong base peak at M-1 peak
due to the loss of terminal hydrogen Alpha cleavage
Mass Spectrometry : Mass Spectrometry Aromatic Hydrocarbons Strong M+ Loss of
hydrogen gives base peak McLafferty rearrangement Formation of benzyl cation or tropylium
ion
Mass Spectrometry : Mass Spectrometry Alcohols M+ weak or absent Loss of alkyl group via
a-cleavage Dehydration (loss of water) gives peak at M-18
Mass Spectrometry : Mass Spectrometry Phenols Strong M+ M-1 due to hydrogen
elimination M-28 due to loss of CO M-29 due to loss of HCO (formyl radical)
Mass Spectrometry : Mass Spectrometry Ethers M+ weak but observable Loss of alkyl
radical due to a-cleavage B-cleavage( formation of carbocation fragments through loss of
alkoxy radicals) C-O bond cleavage next to double bond Peaks at M-31, M-45, M-59 etc
Mass Spectrometry : Mass Spectrometry Aldehyde M+ weak, but observable (aliphatic)
Aliphatic : M-29, M-43 etc McLafferty rearrangement is common gives the base peak A-
cleavage B-cleavage
Mass Spectrometry : Mass Spectrometry M+ strong (aromatic) Aromatic: M-1 (loss of
hydrogen) M-29 (loss of HCO) McLafferty rearrangement is common A-cleavage B-cleavage
Aldehyde
Mass Spectrometry : Mass Spectrometry Ketones Strong M+ A series of peaks M-15, M-29,
M-43 etc Loss of alkyl group attached to the carbonyl group by a-cleavage Formation of
acylium ion (RCO+) McLafferty rearrangement
Mass Spectrometry : Mass Spectrometry Esters M+ weak but generally observable Loss of
alkyl group attached to the carbonyl group by a-cleavage Formation of acylium ion (RCO+)
McLafferty rearrangement Acyl portion of ester OR+ Methyl esters: M-31 due to loss of OCH3
Higher esters: M-32, M-45, M-46, M-59, M-60, M-73 etc
Mass Spectrometry : Mass Spectrometry Carboxylic acids Aliphatic carboxylic acids: M+
weak but observable A-cleavage on either side of C=O M-17 due to loss of OH M-45 due to loss
of COOH McLafferty rearrangement gives base peak
Mass Spectrometry : Mass Spectrometry Aromatic carboxylic acids: M+ Strong A-cleavage
on either side of C=O M-17 due to loss of OH M-18 due to loss of HOH M-45 due to loss of
COOH McLafferty rearrangement gives base peak
Mass Spectrometry : Mass Spectrometry Amines M+ weak or absent Nitrogen rule obey A-
cleavage
Mass Spectrometry : Mass Spectrometry Nitriles M+ weak but observable M-1 visible peak
due to loss of termiminal hydrogen
Mass Spectrometry : Mass Spectrometry Nitro Compounds M+ seldom observed Loss of
NO+ give visible peak Loss of NO2+ give peak
Mass Spectrometry : Mass Spectrometry Alkyl chloride and alkyl bromides Strong M+2 peak
For Cl M/M+2 = 3:1 F or Br M/M+2 = 1:1 A-cleavage Loss of Cl or Br Loss of HCl or HBr
Mass Spectrometry : Mass Spectrometry Alkyl chloride
Mass Spectrometry : Mass Spectrometry Applications of Mass Spectrometry The technique
has both quantitative and qualitative uses. These include identifying unknown compounds,
determining the isotopic composition of elements in a molecule, and determining the structure
of a compound by observing its fragmentation. Followings are the main applications Toxicity of
Toothpastes Measuring nanoparticle size Pharmacokinetics Protein characterization Space
exploration Isotope dating and tracking Molecular weight Bonding Reaction mechanism
Mass Spectrometry : Mass Spectrometry Toxicity of Toothpastes DEG (diethylene glycol)
which is a toxic chemical and usually present in Chinese toothpastes. Measuring nanoparticle
size Mass spectrometry is used to measure nanoparticle size like platinum nanoparticles which
is used as catalyst. Once size of a sphere is measured, its density is also calculated.
Pharmacokinetics Pharmacokinetics is often studied using mass spectrometry because of the
complex nature of the matrix (often blood or urine) and the need for high sensitivity to observe
low dose and long time point data.
Mass Spectrometry : Mass Spectrometry Protein characterization Mass spectrometry is an
important emerging method for the characterization of proteins. The two primary methods for
ionization of whole proteins are electrospray ionization (ESI) and (MALDI). Space exploration
Mass spectrometers are also widely used in space missions to measure the composition of
plasmas. For example, the Cassini spacecraft carries the Cassini Plasma Spectrometer (CAPS),
[44] which measures the mass of ions in Saturn's magnetosphere. Isotope dating and tracking
Mass spectrometry is also used to determine the isotopic composition of elements within a
sample. Differences in mass among isotopes of an element are very small, and the less
abundant isotopes of an element are typically very rare, so a very sensitive instrument is
required. These instruments, sometimes referred to as isotope ratio mass spectrometers (IR-
MS).
Mass Spectrometry : Mass Spectrometry Molecular weight Molecular weight can be
determined by mass spectrometry. Actual number of carbons, hydrogen, oxygen etc By using
relative intensities(peak hight), we can easily calculated the actual numbers of C,H,O etc
atoms. Bonding Bonding can be studied by fragmentation patterns for example, beta cleavage
is possible only if double bonds or heteroatom present. Reaction mechanism Mass
spectrometry is best technique to study reaction mechanism and intermediates produced in
reaction, for example, in carboxylic acid and alcohols a peak at M-18 indicates that water is
produced.
Mass Spectrometry : Mass Spectrometry Determination of Elements Bulk materials such as
steel or refractory metals, elements are determined by low-resolution glow-discharge mass
spectrometry. High-resolution GDMS has been used to study semiconductor materials. GDMS is
considered virtually free of matrix effects. Detection limits in ICPMS as in Table
Mass Spectrometry : Mass Spectrometry Species Analysis Heavy metals in the environment
are stored in complexes with humic acids, can be converted by microbes in different
complexes, and can be transported in live animals and humans. This applies to many elements
such as lead, mercury, arsenic, astatine, tin and platinum For example, tin and lead alkylates
established in soil, water or muscle tissue by GC / MS after exhaustive alkylation or thermal
spray, and ICP-LC/MS API methods.
Mass Spectrometry : Mass Spectrometry Environmental Chemistry the analysis of trace
elements and compounds in environmental samples like air, water, soil etc because of its
detection power, specificity and structural analysis functions Generally, sample preparation is
at least one type of chromatography coupled with MS either offline or online like GCMS
Mass Spectrometry : Mass Spectrometry References Dictionary of Mass Spectrometry, A.I.
Mallet and S. Down, 2009 Introduction to spectroscopy, Donald L. Pavia Hand book of
spectroscopic data, B.D.Mistry. Comprehensive analytical chemistry. . Handbook of
Spectroscopy, by G. Gauglitz and T. Vo-Dinh Instant notes of Analytical chemistry, D.Kealey.
Modern Analytical Chemistry, David Harvey. The Basics of Spectroscopy, David.W.Ball.
Encyclopedia of Analytical Chemistry Applications, Theory and Instrumentation Edited by
R.A.Meyers Handbook of Analytical Techniques edited by Helmut Giinzler and Alex Williams 1st
Edition 2001 Encyclopedia of Spectroscopy and Spectrometry part 2(M-Z) Edited By john C.
lindon, George E. Tranter and John L. Holmes
MS Lesson 4, How to Read a GC-MS Report and Find the [M]
+
 :
The GC-MS data can be presented in different ways. Whatever the format, the essential
data remain the same. A standard GC-MS report is shown on the next page. The report
includes data from the GC chromatogram and data from the MS spectrum. The GC data
tells you how many compounds (qualitative information) were detected in the sample.
The GC data will also give you the quantitative data: the areas of peaks that are detected
in your sample are related to the amount of each compound in the sample. You can use
these peak areas to calculate percent purity of a sample based on GC analysis. The GC
data in a GC-MS report is used to determine the number and amount of the analytes that
pass through the chromatograph. In addition to GC data, the MS records a mass
spectrum for each compound, or peak in the GC. If there were five compounds (peaks)
detected in the GC, then there would be five MS spectra, one for each peak. Obviously,
this means that a GC-MS report will contain lots of information. Much of it is
selfexplanatory.
The first step in evaluation of a GC-MS report is to look over the report to make sure that
the report you received is for the compound you submitted. Does the sample name
correspond to your name? If you see a string of ? characters instead of your name, then
that means that the GC-MS operator could not read your name from the log sheet. You
should always assume that the GC-MS operator does not know you or recognize your
name. Make sure that you print your name in block letters when you fill out the log
sheet. Is the miscellaneous information descriptive of the compound you thought you
were submitting for data collection?
Sometimes MS data is presented along with a computer Library Search Report. The PC
tries to match the spectrum of your analyte to one of the 50,000 spectra that are stored in
the PC MS library. The best fit may (or may not) be your compound. Searching against
the WILEY library (published by WILEY), the computer finds the most likely matches
and lists them. The degree of similarity between the MS spectrum of an analyte and the
spectrum of a known compound in the library is indicated as % Quality. A higher %
means a better match. A match quality of >95% indicates good similarity of the library
spectrum to the spectrum of the analyte being evaluated. But you must exercise caution
in looking over any library match report. The library may have more than one entry for
each compound. In addition, nomenclature used in the library database may not always
be the same for each entry or the same as the name that you are expecting.
Perhaps the most useful presentation of MS spectral data is a numerical data table. A
tabulation of the MS spectrum of 4-nitroacetophenone and the graphical presentation of
the same data are shown on the previous pages in this manual. The structural formula
will not be part of GC-MS reports that you receive for your samples. The tabulated data
is needed to determine intensities of ions detected at each mass/charge value. The
compound 4-nitroacetophenone, has a molecular formula of C8H7NO3. Since the
compound has an odd number of nitrogen atoms, its [M]
+
has an odd value for
mass/charge. As you look at the MS data presentations, you will immediately notice that
MS spectra
have lots of peaks. Furthermore, each peak has two notable features: different m/z values
and different sizes (intensities). For the time being, we only need to consider one of the
peaks. That one peak is, of course, the molecular ion peak. If you know the structure of
the analyte, finding the [M]
+
should be easy, provided that the compound is one of the
85% of organic compounds that has molecular ions in electron impact MS spectra.
Calculate the expected m/z value and then look for it. It is, of course, more difficult to
identify the [M]
+
ion if you do not already know the structure of the compound. In any
event, you must try to find the [M]
+
ion in the MS data first. The rest of MS
characterization depends upon this first step.
In the easiest cases, the [M]
+
ion is the largest (highest/most intense) peak at the highest
m/z value. Not the highest peak, but the highest peak at the highest m/z. It is important
to
remember that the [M]
+
ion does not have to be the most intense ion, but it should be the
most intense signal (highest line) in the cluster of peaks at the highest m/z values.
The differing intensities of cations detected by the mass spectrometer are proportional to
the relative stabilities of the cations. Really stable cations show up as really large peaks,
unstable cations are either very small peaks or they do not show up at all. About 15% of
the time, the [M]
+
is not seen because it is not stable enough. At other times, the [M]
+
is
seen, but there are contamination peaks with higher m/z values that are also seen.
Contamination peaks indicate a dirty MS, not a dirty sample. You have to learn by
experience what the contaminant peaks in a MS from a particular instrument to expect.
While examining peaks in a MS data set, you will notice that one peak is always larger
(more intense/higher) than the others. The largest peak is significant, and we will learn
about it later. For the time being, it is enough to know that there is a largest peak in any
MS and that this most intense peak is called the base peak. It is also very important to
remember that the molecular ion (also called a parent ion) may or may not be the base
peak. All peaks with a lower value for m/z than the parent ion, [M]
+
, are smaller charged
cations (known as fragment or daughter ions) that have mass/charge values less than the
mass/charge value of the molecular ion. The fragment ions are made by loss of atoms
from the molecular ion. The types of peaks that may be present in a mass spectrum are
listed in Table III-2, on the next page. We will learn about fragmentation processes and
how they occur in later lessons. Base Peak
The most intense peak in a MS spectrum.
Parent Peak
The molecular ion peak in a MS spectrum.
Fragment Peaks

Peaks formed by the fragmentation of the

parent peak that have m/z values less than
that of the parent ion but which might have
a greater intensity than the parent ion has.
Table III-2. Terms for Ion Peaks That Must Be Memorized. MBM

At this point you will be expected to know that a MS spectrum definitely has a base peak,
it will also have fragment ions, and hopefully it will also have a parent (molecular) ion.
You are also expected to know how to predict a reasonable Lewis structure of a [M]
+
for
a known compound. You should also be able to calculate the m/z value of a [M]
+
of a
known structure. Now, you must learn how to perform the first step in analysis of MS
spectral data, finding the [M]
+
ion. If present, it will be the largest peak in the cluster
of peaks with the greatest m/z values.
Q17. What are the values of m/z for the [M]
+
and the base peak in the following tabulated MS
data?
m/z abundance
108 0.20
107 9.20
106 100
105 56
93 35
43 87
Q18. What are the values of m/z for the [M]
+
and the base peak in the following tabulated MS
data?
m/z abundance
176 11,124
175 194,202
134 16,213
91 2,000,194
77 500,950
65 154,234
A17.
[M]
+
= 106 m/z.
Base peak = 106 m/z
The peak at 106 has the highest intensity of the
peaks with the largest m/z values (from 105 to
108) in this data set. The peak at m/z of 106
also happens to be the peak of greatest intensity
in the entire data set.

Q19. What are the values of m/z for the [M]

+
and the base peak in the following tabulated MS
data?
m/z abundance
97 1.1
96 98.9
95 1.1
94 100
93 80
81 45
79 46
15 50
A18.
[M]
+
= 175.
Base peak = 91
The molecular ion is the largest of the high m/z
peaks (175 & 176). The base peak is the largest
signal detected, in this case at a m/z of 91. The
abundance values are unitless. If normalized to
the abundance of the largest peak, the values
would range from 100 (for the largest) to 0.56
for the smallest peak at m/z of 176.
(11,124/2,000,194)*100 = 0.56
A19.
m/e of [M]
+
= 94
m/e of base peak = 94
The molecular ion and base peak are the same in
this example. The peculiar feature of this data
set is the appearance of a nearly equal intensity
peak in the high m/z ion range (at 96). There is
a very rational explanation for this, which we
will cover in a future MS lesson. For now, just
remember to look at the peaks with the highest
m/z values and focus in on the most intense of
them as the likely [M]
+
signal.