PRACTICE SUMMATIVE ASSESMENT

Principles of Mass Spectrometry

INT2010

Academic Year: 2020-2021

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Faculty of Science and Engineering

Maastricht Science Programme

 2020 Maastricht University

Nothing in this publication may be reproduced and/or made public by means of printing, offset, photocopy or
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 1. When comparing the intensities of a set of peaks between spectra it is common to use a
window for every peak to compensate for small mass errors (shifts) between spectra. Would
you choose a dynamic window width which is dependent on the m/z value (e.g. in ppm) or a
fixed window width? Explain your choice for TOF and FT-ICR data.

2. What is the opportunity and are the two dangers of multi-variate data, as provided by mass
spectrometry, for data analysis (in specific classification and statistics)?

3. Name two advantages and two disadvantages of hierarchical clustering.

4. What is the shape of ion cloud in FT ICR cell during detection?

a. Thin thread in a radial direction
b. Rotating thin ring
c. A cylinder along the direction of magnetic field

Answer Letter:

5. What is the shape of ion cloud in the Orbitrap analyzer during detection?
a. Thread parallel to the axis of the trap rotating around the central electrode
b. Thread in radial direction that rotates around the central electrode and bounces along
it
c. Rotating thin ring that bounces along the axis
d. A thin cylinder rotating around the axis

Answer Letter:

6. What method is used to excite axial oscillations of ions in the Orbitrap analyzer?
a. AC waveform applied to the outer electrodes
b. A voltage pulse on the central electrode applied after ions entered the trap
c. Off-equator entry into the increasing electric field of the trap
d. An extraction voltage pulse on the C-trap

Answer Letter:

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 In a negative mode mass spectrum, there is a peak at m/z 367.141198. Based on accurate
mass alone, there are four possible elemental formulae within 10ppm (limited to CHONS ).
Peak Mass Intensity (norm)
Monoisotopic peak 367.141198 1

A+1 Peaks 0.999385 0.015782

(Mono mass plus) 1.003355 0.210813
1.006306 0.004007

A+2 Peaks 1.995796 0.088612

2.002625 0.002599
(Mono mass plus) 2.004285 0.005251
2.006711 0.020948

Reference data:
Name Symbol Mass Abund (%).
Carbon C(12) 12.000000 98.90
Carbon C(13) 13.003355 1.10
Hydrogen H(1) 1.007825 99.99
Hydrogen H(2) 2.014102 0.015
Oxygen O(16) 15.994915 99.76
Oxygen O(17) 16.999131 0.038
Oxygen O(18) 17.999159 0.20
Nitrogen N(14) 14.003074 99.63
Nitrogen N(15) 15.000109 0.37
Sulfur S(32) 31.972072 95.02
Sulfur S(33) 32.971459 0.75
Sulfur S(34) 33.967868 4.21
Sulfur S(36) 35.967079 0.020

7. Considering the isotopic fine structure, one of the potential assignments is much more likely
than the others - identify the correct formula.
a) C18H23O8-
b) C15H27O8S
c) C19H27O3S2-
d) C16H31O3S3-
e) C15H29NO3S3

Answer Letter:

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 8. Estimate minimum resolving power R that is needed to baseline resolve 13C isotopic pattern of:

a) a singly-protonated peptide with MW=2 kDa;

Answer:

b) a doubly-protonated peptide with MW=2 kDa;

Answer:

c) a small protein with MW=20 kDa carrying 20 protons;

Answer:

9. Rank the following ion beams in order of descending subsurface damage:

a) Gallium ion beam
b) Water cluster ion beam
c) C60 molecular ion beam
d) Argon cluster ion beam
e) Bi3 ion beam

Most damage: ; ; ; ; Least damage

10. List five mass analyzers. Which detector would you use with these mass analyzers?

11. Describe at least three analytical features that differentiates SIMS from MALDI

12. Assuming a flight length of 5.0 m and a sample introduction potential of 8 kV, how long (in μs)
would it take for an ion of 2011.56 m/z to reach the detector?
μs

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 Below are the results of four ion simulations (labeled I – IV) of ions in a quadrupole cross-
section. The electrodes of the quadrupole are the four half-ellipses on the edges of each
simulation. The start of each ions’ trajectory is indicated by a small circle. All simulations
are identical in all aspects (e.g., quadrupole voltage, ion start position and velocity, length
of the simulation, etc.) except for the ions’ mass-to-charge ratios that are: 100, 300, 500
and 700 m/z.

13. Which ion m/z corresponds to each of the depicted simulations (Complete the table below with
the correct m/z value)?
Simulation I: m/z
Simulation II: m/z
Simulation III: m/z
Simulation IV: m/z

14. If the frequency of the quadrupole were doubled, would this most likely:
A) Increase the stability of the simulated high m/z ions
B) Decrease the stability of the simulated high m/z ions
C) Increase the stability of the simulated low m/z ions
D) Decrease the stability of the simulated low m/z ions

AnswerLetter:

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 15. One of these simulations required far fewer computations than the others. Which one was the
simplest to compute and why?

16. The shaded and unshaded electrodes are electrically coupled. The top and bottom electrodes
began the simulation as -40 V. The left and right electrodes began the simulation as +40 V. No
voltage offset (i.e., a DC offset) was applied. Would inverting the starting electrodes, so the left
and right electrodes began as -40 V and the top and bottom electrodes began as +40 V alter
the stability of the simulated ions? Why or why not? What if the ions simulated were negatively
charged?

The figure below depicts a two-dimensional, orthogonal Time-of-Flight mass

spectrometer. All electrodes are static. The electrodes are labelled (I: unshaded, II:
vertically-shaded, and III: diagonally-shaded) and ion paths are labeled (A: solid line, B:
short-dashed line, and C: long-dashed line). All ion paths start in the lower-left quadrant
and move to the right.

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 17. Assuming positively charged ions, which configuration of electrodes (I, II, and III) is most likely
to produce flight paths A, B, and C? (Please write “A”, “B”, and “C” only once each below. The
remaining four options should be blank).

Case 1; I: 1 kV II: -10 kV III: -10 kV

Case 2; I: 1 kV II: -10 kV III: 10 kV

Case 3; I: 10 kV II: 1 kV III: 1 kV

Case 4; I: 1 kV II: -1 kV III: -1 kV

Case 5; I: 10 kV II: -10 kV III: 10 kV

Case 6; I: 1 kV II: 1 kV III: 1 kV

Case 7; I: -1 kV II: -10 kV III: 1 kV

18. Which of the following terms best describes electrode III?

A) A pusher
B) An electron multiplier
C) A voltage divider
D) A reflectron
E) A Time-of-Flight mass spectrometer
F) An ion funnel

Answer Letter:

19. Ion path “B” looks parabolic near electrode III. At the vertex of its parabolic curve, the ion
producing path “B” has:
A) Mostly potential energy
B) Mostly kinetic energy
C) Only kinetic energy
D) Only potential energy
E) Equal kinetic and potential energy
F) No kinetic or potential energy

Answer Letter:

20. An einzel lens is an ion optical element:

a) consisting of one singular electrode.
b) consisting of three electrodes.
c) employed in an otherwise field free region, e.g. in a TOF.
d) used to focus ions into a coherent beam and change their initial energy.
e) used to focus ions into a coherent beam without changing their initial energy.

All letters that apply:

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 A protein is analyzed using mass spectrometry. The following peaks are highly prominent in
the mass spectrum:
1917.06 m/z
1797.25 m/z
1691.53 m/z
1597.56 m/z
1513.47 m/z
1437.80 m/z
1369.33 m/z
1307.09 m/z
1250.26 m/z

21. What is the molecular weight of the protein?

22. What are the charge states of the 1250.26 m/z and 1797.25 m/z peaks?

23. What is the most likely ionization method used to generate this protein mass spectrum?
A) MALDI
B) CID
C) PCA
D) ESI
E) EI

24. Explain one function of PCA when it is used to work with mass spectrometry data.

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 The mass spectrum below is a simulated fragmentation of a peptide with a molecular mass
of 616.2513

25. Assuming that the peak at m/z 215.1144 corresponds to the a2 fragment ion, what is the
identity of the amino acid lost between the a3 and a2 fragment ions?

26. Assuming that the peak at m/z 511.2087 is the b4 fragment ion, what is the identity of the
amino acid lost between the intact peptide ([M+H+] ion at 616.2513) and the b4 fragment ion?

27. Although b1 fragments are not found in normal peptide fragment spectra, in this simulated
spectrum there is a b1 fragment peak. The b1 fragment ion contains the residue of a glutamine.
If this glutamine were removed by cleavage of the b1/y bond and an isoleucine residue were
added at the carboxy terminus, what would the m/z of the resulting ion be?

28. For a hexapeptide, if a PTM were added to the amino acid lost between the y3 and y2
fragments, which y and b fragment ions would be different than if no PTM were added?

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 Shown below are the EI-MS (electron ionization) spectrum and the structure of an alkaloid
widely adopted as spice. The most prominent peaks in the spectrum have been labelled
with their respective m/z-values.

29. Assuming a singly charged species, what type of mass do the m/z values represent? Choose
one answer.
A) molecular mass
B) exact mass
C) accurate mass
D) average mass
E) nominal mass

Answer Letter:

30. The base peak is:

A) m/z 285 because it has the highest m/z-value.
B) m/z 201 because it has the highest intensity.
C) m/z 285 because it represents the molecular ion.
D) m/z 201 because it represents the molecular ion.
E) not represented in this spectrum.

Answer Letter:

31. There is an m/z 84 neutral loss from m/z 285 to 201 but the spectrum also shows an m/z 84 ion.
Explain and use pseudo sum formulae to describe fragments (e.g. A3BC2D).

32. Starting from m/z 201, what chemical losses lead to the fragments m/z 173, 143, and 115?

173 m/z : 143 m/z : 115 m/z :

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 You are working in a laboratory that regularly performs experiments on DESI-QqQ
(Desorption electrospray ionization triple quadrupole) instruments and just recently
received time-critical samples. As you are about to start your measurements, you notice
that someone left the instrument running and you are out of solvents. Usually you are
running a mixture of 50/50 (v/v) methanol / water with 1% formic acid added. Checking your
stocks, you notice that your missing methanol but there is plenty ethanol available.

33. Describe the basic principle of ESI. What is the difference to DESI and what type of
measurements is DESI suited for?

34. Describe the basic principle behind a QqQ-MS (triple quad mass spectrometry) instrument.

35. What are the possible ramifications of using ethanol instead of methanol in the solvent
mixture? Elaborate.

Insulin has a molecular formula of C 256H381N65O76S6 and a molecular weight of 5778 g/mol.
Some exact masses of some elements are:
[12C = 12.00000 Da; 13C = 13.00335 Da; 14N = 14.00307 Da; 15N = 15.00011 Da;
16O = 15.99491 Da; 18O = 17.99916 Da; 1H = 1.007825 Da; e- = 0.000549 Da;

32S = 31.97207]

36. What mass resolution is needed to baseline resolve protonated insulin from its sodiated
counterpart?

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 37. If someone measured the molecular weight of insulin instead of its exact mass, what would
their mass error be (in ppm)?

38. What are some differences between ECD and CID? What fragments might you expect with one
method vs the other? Elaborate.

Iodine has a single stable isotope at 126.904 Da. Bromine has two stable isotopes at 78.918
(50.7% abundant) and 80.916 (49.3% abundant) Da.

39. If bromine and iodine were capable of forming stable clusters of 5 atoms (Br5 and I5), assuming
everything else equal, how much taller would a peak of 5I appear than a peak of Br5?

40. What is the PPM error of assuming Bromine (both isotopes) or Iodine are their nominal mass?

Bromine 79: Bromine 81: Iodine 127:

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