• two essential steps
◦ making ions
◦ separating ions by mass (mass/charge ratio: m/z)
• M+ = molecular ion (also known as radical cation)
• we can give the molecular an excess of energy which may cause
fragmentation of molecular ion (m+ and n+) smaller pieces of original
molecule, therefor smaller ion
• in most cases, the Z (charge of individual species) is +1. therefore separation
can be separated based on the actual mass. if dication, will be based on half
the mass because it would be +2.
• displays the number of ions to create a spectrum
• slide 3: tallest peak in the spectrum is at 77, known as the base peak. on the
vertical axis, the unit is % of base peak - intensities are relative. assign the
tallest peak (base peak) of the spectrum at 100%. base peak in sample is not
the molecular ion. it's actual the peak where it says 121. this suggests that
fragmentation is more likely for this particular molecule instead of surviving
intact to the detector. the horizontal axis is not g/mol.
• slide 4: 4 steps. in most cases, the 4 stages are present in every single mass
spectrometer. steps 2 and 3: how to make ions and how to separate them.
key steps that dictate whether you know what the molecule is or not.
• slide 5: ionization techniques
◦ a) gas phase method
▪ popular. 1st to be developed and relatively cheap. but there are
▪ must work in gas phase - get sample molecule in gas phase,
must be volatile. min vapour pressure of 10^-6 Torr.
▪ works really well for non-ionic organic compounds (no salts)
and low molecular masses (<1000 Da)
◦ electron impact (EI)
▪ electron beam - extremely high energies (70 eV)
▪ introduce sample vapour - bombarded by highly energized
electron beam. the collision end up ejecting molecules. leaves
behind a radical cation/molecular ion. ▪ creating a molecular ion with an excess of 55 eV -
fragmentation is a problem because of this.
▪ number 1 consequence is fragmentation
◦ chemical ionization (CI)
▪ "softer" technique
▪ indirect ionization, not going to bombard molecule directly
▪ use of a reagent gas - use electron beam and shoot the gas and
create ions from the methane and shoot those ions at the target
▪ CH4 > CH4 .+ + e- CH4.+ + M > CH3. + [M-H]+
▪ [M+1]+ is the quasimolecular ion
▪ transferring lower quantities of energy (<5 eV)
◦ comparison of EI and CI spectra
▪ top: lots of fragmentation. base peak is not molecular ion. base
peak = 165. lost a CH3, most popular ion was the molecule
without a methyl group (base peak)
▪ bottom: extra peaks are adducts. instead of simply transferring
an atom, you can get a reaction. the peaks should be small.
▪ if you wanted to eliminate the adducts, use less methane. the
concentration of adducts is generally proportional to the
partial pressure of the methane you use.
▪ CI spectrum gives you the quasimolecular ion was 117,
therefore 117 - 1 = 116. molecular is so fragile that none of it
reached the detector which is why it didn't show up on the
◦ b) desorption ionization methods
▪ condensed phase
▪ appropriate for molecules which cannot be analyzed by gas
phase i.e. big molecules and non volatile. no fragmentation
◦ field desorption
▪ metal emitter covered with micro needles. coat micro needles
with sample molecule. turn on the voltage (extremely high)
which turns metal needle into anode. electrons is stripped from molecule. creates molecular ion. because it is an anode.
electrostatic repulsion lifts molecule away because it is
▪ advantage gives you a very clear molecular ion peak.
disadvantage is there is no fragmentation which means there is
no extra info other than the molecular mass.
◦ fast atom bombardment (FAB)
▪ uses a beam of atoms. dissolve sample in a "matrix" (solvent,
gel, etc). the purpose of the matrix is to protect molecular to
minimize fragmentation and stabilize molecule. bombard
sample with atoms (xenon or argon). volatilize and ionize
molecules at the same time. depending on the matrix, proton
transfer to and from. 2 quasimolecular peaks representing
addition or subtraction to and from the matrix. peaks around
(one on either side) depending. useful for large biomolecules.
▪ can get some fragmentation at very predictable points
▪ disavantage is the matrix itself (see extra peaks)
◦ laser desorption
▪ firing a laser, but similar to FAB
▪ limitation for MALDI is 3kDa, small compared to FAB.
◦ c) evaporative ionizatin
▪ i) thermospray: grossly unpopular
▪ ii) electrospray (ES)
▪ capillary, dissolve sample in a solvent (volatile solvent).
comes down to increasingly narrow tube. creates
droplets containing ions. over a short period of time,
you have a volatile solvent that is evaporating, droplets
become smaller. individual cations are coming closer
together because solvent is evaporating away. more and
more electrostatic repulsion. repulsions overcomes
adhesion properties of the solvent and you get a
coulombic explosion generate isolated ions.
▪ disadvantage: aqueous solvent, formation of adducts
with other cations present in the solution (explains
really big peak).
• ion separation methods (3rd stage) ◦ analyzer: separate ions
◦ magnetic sector (oldest, cheapest, most popular)
▪ send in stream of positive ions. apply a magnetic field to the
path of those ions. magnetic field will being cations. deflecting
force is Bvz (b is force of magnetic field, v is velocity and z is
charge) since it is mostly similar, B is the dictation - greater
deflation force, larger curve in their trajectories. lighter ions
curve more, heavier ions curve less. both hit the detractor at
another point. count the number of collisions at the detector on
the specific position and plot them. relative proportions.
▪ 4 parallel rods with a hole down the middle. apply an
alternating current to the 4 individual rods. molecular ion is
fed into the mouth of the 4 rods. the positively charged ion will
be attracted to one of the negatively charged electrodes
(cathode). in the next instant, we change the polarity of the 2
rods (because it is alternating). the ion then becomes attracted
to the changed cathode. then the polarities change again, so
molecular ion moves again. constantly changing the trajectory
of the cation as impasses through the 4 rods - creates a spiral
trajectory. makes resonant ions towards the detector. the
smaller the ion, the longer it travels through the tube. the
bigger the ion, the faster it travels through the tube.
◦ time of flight
▪ lighter ions travel thorough the chamber faster than fatter ions.
mass range is unlimited. can get an exact mass. disadvantage is
that it's expensive.
• slide 27: the isotopomers