MS

Question 1

Hvad er N-terminal (Aminoterminal)

Answer 1

• Det er starten af peptidet.
• Her sidder den frie aminogruppe (-NH₂).
• Når man skriver en aminosyresekvens, starter man altid med N-terminalen til venstre.

Question 2

Hvad er C-terminal (Carboxyterminal)

Answer 2

• Det er enden af peptidet.
• Her sidder den frie carboxylgruppe (-COOH).
• Slutningen på aminosyrekæden.

Question 3

Generally, ionization of peptides by ___1___ will produce multiple charged ions ([M+nH]n+; n>1), whereas ionization by ___2___ will generate singly charged ions ([M+H]+).

Answer 3

1 = ESI
2 = MALDI

Question 4

A reflectron can be used in a ___1___ mass analyzer to improve ___2___

Answer 4

1 = TOF
2 = resolution

Question 5

The matrix used in UV-MALDI ionization must encompass an ___1___ to absorb the energy provided by a ___2___

Muligheder:
“double bond” - “laser” - “infrared light” - “ion beam” - “aromatic core” - “halogen” - “organic acid” - “heated filament”

Answer 5

1 = aromatic core
2 = laser

Question 6

A sodium adduct of a molecular ion [M+Na]+ has been determined to m/z(monoisotopic) 1440.692.

Calculate the m/z(monoisotopic) value of the doubly-charged ion [M+2H]2+ (3 decimals accuracy must be provided)

Answer 6

Svar: 709.859

[M+Na]+ = 1440.692 => M = 1440.692 - 22.989769 = 1417.702 Da
[M+2H]2+ = (1417.702 + 2*1.007825)/2 = 709.859

Question 7

A total ion chromatogram (TIC) shows the ___1___ as a function of ___2___

Muligheder (der er 3 muligheder til hver af de to):
1) “sum of all ion intensities in a spectrum” - “base peak intensity in a spectrum” - “intensity of a specific ion in a spectrum”
2) “charge state” - “column retention time” - “m/z”

Answer 7

1 = sum of all ion intensities in a spectrum
2 = column retention time

Question 8

In a time of flight (TOF) mass analyzer ___1___ ions will be detected before ___2___ ions

Muligheder:
“large” - “small”

Answer 8

1) small
2) large

Question 9

According to the Nitrogen rule, an odd number of N is associated with an ___1___ nominal mass.

Muligheder:
Odd - Even

Answer 9

Odd

Question 10

A mass spectrometer measures the ___1___ and the relative ___2___ of ___3___

Answer 10

1 = m/z
2 = abundance
3 = ions

Question 11

In proteomics, ___1___ is used to separate ___2___ in a complex sample.

The separation and analysis of a particular ion can be evaluated by using a ___3___

Answer 11

1 = Liquid chromatography
2 = peptides
3 = extracted ion chromatogram

Question 12

Calculate the relative mass accuracy (in ppm; two decimals) of an instrument provided the following data:

m/z(experimental): 1382.5401
m/z(calculated): 1382.5199

Answer 12

Svar: 14.611

Formel: Massepræcision (ppm) = ((Eksperimentel m/z - Beregnet m/z) / Beregnet m/z) *10^6

Question 13

Which of the following statements are true regarding mass spectrometry?

(multiple answers allowed)

a) Atomic mass is the most accurately defined molecular mass.
b) Only ionized species can be measured using mass spectrometry.
c) Monoisotopic mass is the most accurately defined molecular mass.
d) A mass spectrum signal intensity corresponds to abundance.
e) Mass spectrometry only deals with singly charged species
f) The monoisotopic peak can always be seen in a mass spectrum for a given compound.
g) The monoisotopic peak is not always present in a mass spectrum for a given compound.

Answer 13

Svar: b, c og g

Question 14

Mass spectrometers are highly sensitive instruments.

Select the correct statements below (multiple answers allowed):

a) The reflectron provides higher sensitivity
b) Fourier transformation of data generates high sensitivity
c) The multi channel plate provides high sensitivity
d) A long flight path provides high sensitivity
e) Sensitivity is obtained by secondary electrons that amplify the incoming signal

Answer 14

Svar: c og e

Question 15

Identify elements existing as monoisotopic elements (multiple answers allowed)

a) Nitrogen (N)
b) Phosphorus (P)
c) Hydrogen (H)
d) Sodium (Na)
e) Oxygen (O)
f) Fluor (F)

Answer 15

Svar: b, d og f

Question 16

A MSMS fragmentation spectrum has been generated of a small peptide ion ([M+H]+) of m/z 698.3580
It is known that the peptide encompasses 6 residues with a C-terminal arginine (R) residue
The following ions has been detected:

Fragment ions:
b1: 88.040
b2: 217.082 y5
b3: 316.151 y4
b4 y3: 383.215
b5 y2: 312.178
y1: 175.119
Determine the correct sequence based on a table of residue masses:
___ - ___ - ___ - ___ - ___ - arginine

Answer 16

1 = serine
2 = glutamic acid
3 = valine
4 = alanine
5 = histidine

b-ions: Residue masse +H
y-ions: Residue masse +2H + OH

Question 17

A triply charged ion (M+3H)3+ is detected at m/z 581.636 (monoisotopic mass).

Calculate the molecular mass of the analyte (3 decimals required).

Answer 17

Svar: 1741.885

(581.636 * 3) - (3 * 1.007825) = 1741.8845

Question 18

Electron ionization can be regarded as a soft ionization technique

Muligheder:
“Sandt” - “Falsk”

Answer 18

Falsk

Question 19

Fragmentation of a peptide bond in tandem mass spectrometry will produce ___1___ representing the N-terminal fragments and ___2___ representing the C-terminal fragments.

Answer 19

1 = b ions
2 = y ions

Question 20

Calculate the nominal mass of pentanoic acid (find elemental masses in appendix “Elemental masses”

Hint: sumformel C5H10O2

Answer 20

Svar: 102

(5 * 12)+(10 * 1)+(2 * 16) = 102

Question 21

Carboxylic acids are unstable in GC-EI-MS (low intensity molecular ion), but are also reactive. You are not able to eliminate side-reactions during analysis. In order to determine conversion rate (and thus yield) from your synthesis, you therefore decide to derivatize before analysis. You chose to do TMS (trimethylsilyl, SiMe3) derivatization, where the acid hydrogen is substituted for TMS.

Calculate the nominal mass for the TMS derivate of pentanoic acid

Answer 21

Svar: 174

Pentansyre: C5H10O2
TMS = trimethylsilyl: Si(CH3)3 = SiC3H9

Ved TMS-derivatisering udskiftes det sure hydrogen i carboxylgruppen (-OH) med en TMS-gruppe, så man får:
C5H9O2SiC3H9 -> C8H18O2Si

Question 22

Methionine residues are often found to be oxidized in isolated proteins and peptides. The oxidation adds 16 Da to the residue mass of methionine.

A tryptic peptide of 7 residues encompassing one methionine residue has been subjected to MSMS analysis and the fragment ions indicated below were detected.

Fragment ions:
b1: 116.035
b2: 173.056 y6
b3: 272.125 y5
b4 y4
b5: 548.203 y3: 363.187
b6 y2: 234.145
y1: 147.113
Identify the peptide sequence and indicate if the methionine residue has been oxidized (MethionineOX) or not (Methionine)
___ - ___ - ___ - ___ - ___ - ___ - ___

Answer 22

1 = aspartic acid
2 = glycine
3 = valine
4 = methionineOX
5 = glutmaic acid
6 = serine
7 = lysine

b-ions: Residue masse +H
y-ions: Residue masse +2H + OH

M(Ox) mass (Da) = 147.035
For at teste at det er M(Ox) regnes først:
b5 - b3 = 548.203 - 272.125 = 276.078
Dette passer med:
M(Ox) + E = 147.035 + 129.043 = 276.078

Question 23

Acetaminophen/Paracetamol (C8H9NO2) is the active component in pain killers like Pamol and Panodil.

Calculate the monoisotopic mass of acetaminophen (3 decimal accuracy)

Answer 23

Svar: 151.063

(8 * 12.0) + (9 * 1.007826) + (1* 14.003074) + (2* 15.994915) = 151.063

Question 24

An [M+H]+ ion is detected in a mass spectrum.

The corresponding sodium adduct [M+Na]+ will present a mass increase of (only one answer allowed):

Muligheder:
a. 22.9898
b. 23.9977
c. 21.0746
d. 21.9819

Answer 24

Svar d. 21.9819

The mass of sodium is 22.989769. The difference between the ions is then 22.989769 - 1.007825 = 21.98194

Question 25

Electron ionization of a neutral use ___1___ to predominantly generate a ___2___ ion which is a ___3___ Muligheder: 1) accelerated argon atoms - a laser - a beam of electrons - low pH 2) positive single-charged ion - negative single-charged ion - protonated 3) radical - fragment - dimer

Answer 25

Svar: 1) a beam of electrons 2) positive single-charged ion 3) radical

Question 26

An MSMS fragmentation spectrum has been generated of a small peptide ion ([M+H]+) of m/z 662.32. It is known that the peptide encompasses 7 residues with a C-terminal arginine (R) residue The following ions has been detected: Fragment ions: b1: 102.056 b2: 159.077 b3: 273.120 b4: 344.157 y1: 319.172 y2: 262.151 y3: 175.119 Determine the correct sequence based on a table of residue masses: ___ - ___ - ___ - ___ - ___ - ___ - arginine

Answer 26

Svar: [theronine] - [glycine] - [asparagine] - [alanine] - [glycine] - [serine] - arginine

Question 27

In time-of-flight (TOF) mass spectrometry the ___1___ of an ___2___ is determined by a measurement of the ___3___ Muligheder: 1) magnetic momentum - m/z value - mass - gyromagnetic ratio - charge 2) uncharged particle - molecule - ion - isotopic distribution - mass 3) Trajectory curve - Frequency - Oscillation frequency - time-of-flight

Answer 27

Svar: 1) m/z value 2) ion 3) time-of-flight

Question 28

Fragmentation of a peptide of 13 residues in MSMS analysis produced the two fragment ions (m/z values given): y4: 455.269 y5: 602.337 Identify the amino acid residue defined by these y-ions and provide the position of this residue in the peptide (numbering from N- to C-terminus): Amino acid: ___1___ Position in peptide: ___2___ Muligheder: 1) Pro - Trp - Asn - Met - Phe - Ile - Val - Gly 2) 9 - 6 - 15 - 7 - 12 - 1 - 2

Answer 28

Svar: 1) Phe 2) 9

Question 29

The presence of a specific analyte in an LC-ESI-MS analysis can be evaluated by ___1___ Muligheder: a) Electron ionization b) a base peak chromatogram c) a total ion chromatogram d) MALDI - an absorption spectrum e) an extracted ion chromatogram

Answer 29

Svar: e) an extracted ion chromatogram

Question 30

The matrix used in UV-MALDI ionization must encompass an ___1___ to absorb the energy provided by a ___2___ Muligheder for begge: a) halogen b) organic acid c) aromatic core d) infrared light e) laser f) heated filament g) double bond h) ion beam

Answer 30

Svar: 1 = c) aromatic core 2 = e) laser

Question 31

A sodium adduct of a molecular ion [M+Na]+ has been determined to m/z(monoisotopic) 1237.892. Calculate the m/z(monoisotopic) value of the doubly-charged ion [M+2H]2+ (3 decimals accuracy must be provided)

Answer 31

Svar: 608.459 [M+Na]+ = 1237.892 => M = 1237.892 - 22.989769 = 1214.9022 Da [M+2H]2+ = (1214.9022 + 2*1.007825)/2 = 608.459

Question 32

A reflectron can be used in a ___1___ mass analyzer to improve ___2___ Muligheder: 1) orbitrap - quadrupole - TOF 2) analysis time - sensitivity - resolution

Answer 32

Svar: 1) TOF 2) resolution

Question 33

An amino acid substitution in a protein supports the development of disease. The variant residue is encompassed in the tryptic peptide: Normal: GGNEESTK Sickle cell disease: GGNAESTK The protein was isolated from an individual, digested with trypsin and analyzed by MSMS. The observed fragment ions of the peptide are indicated below. Observed y-ions ion m/z y1: 147.113 y2: 248.160 y3: 335.193 y4: 464.235 y5 : y6 : y7: 764.342 Answer the following questions: 1. Calculate the m/z value of the y5-ion: ___1___ 2. Based on this analysis, it can be concluded that the individual express the ___2___ Muligheder: 1) 603.298 - 593.278 - 569.280 - 601.365 2) Disease-causing variant - Normal variant

Answer 33

Svar: 1) 593.278 2) Normal variant

Question 34

Fragmentation of a peptide bond in tandem mass spectrometry will predominantly produce ___1___ representing the N-terminal fragments and ___2___ representing the C-terminal fragments. Muligheder for begge: a) c ions b) x ions c) z ions d) b ions e) y ions f) a ions

Answer 34

Svar: 1 = d) b ions 2 = e) y ions

Question 35

When a triple quadrupole instrument is operated in product ion scanning, the first quadrupole is ___1___ and the third quadrupole is ___2___ Muligheder for begge: a) aet in scanning mode b) set as a collision cell c) set to a fixed m/z value

Answer 35

Svar: 1 = c) set to a fixed m/z value 2 = a) set in scanning mode

Question 36

A peptide is analyzed by ESI-MS and detected as an [M+2H]2+ ion. Indicate the distance between ions in the isotopic cluster. Muligheder: a) 2 b) 0.33 c) 0.5 d) 1

Answer 36

Svar: c) 0.5

Question 37

A mass spectrometer measures the ___1___ and the relative ___2___ of ___3___. Muligheder for alle: a) absolute abundance b) molecules c) m/z d) z e) magnets f) charge state g) abundance h) elements i) ions j) mass

Answer 37

Svar: 1 = c) m/z 2 = g) abundance 3 = i) ions

Question 38

A peptide from a protein has a calculated mass of 2478.132 Da. This peptide contains a threonine residue (Thr). In some individuals carrying a modified protein, this residue has been exchanged for an alanine residue (Ala). Calculate m/z (monoisotopic) of the given peptide carrying the Ala residue (3 decimal accuracy).

Answer 38

Svar: 2449.129 Thr: monoisotopisk masse = 101.0477 Ala: monoisotopisk masse = 71.0371 Masse substitution: Δm = 71.0371−101.0477 = −30.0106 Da Peptidet bliver lettere med 30.106 Da Udregn ny masse: 2478.132−30.0106 = 2448.1214Da Så skal massen findes for [M+H]+ (singly charged): m/z = 2448.1214+1.0073 = 2449.129

Question 39

Fragmentation of a peptide bond in tandem mass spectrometry will produce ___1___ representing the N-terminal fragments and ___2___ representing the C-terminal fragments. Muligheder for begge: a) c ions b) x ions c) z ions d) b ions e) y ions f) a ions

Answer 39

Svar: Svar: 1 = d) b ions 2 = e) y ions

Question 40

A protein is digested by trypsin at a condition where all susceptible bonds are cleaved. The generated peptides are analyzed by MALDI MS. With respect to evaluation of ion intensities, please select the correct statement(s) below. Muligheder: a) All peptide-ions will have the same intensity as they are present at the same molar ratio b) The ion intensity correlates with amount c) Not all peptides from the digest will be detected d) The detected peptide-ions will present different ion intensities e) The ion representing the N-terminal peptide will not be visible

Answer 40

Svar: c og d

Question 41

Select the correct monoisotopic mass of the disaccharide sucrose (C12H22O11). Muligheder: a) 344.1162 b) 344.2162 c) 342.2162 d) 342.8162 e) 342.1162

Answer 41

Svar: e) 342.1162 12 * 12 + 22 * 1.007825 + 11 * 15.994915

Question 42

Calculate the relative mass accuracy (in ppm; two decimals) of an instrument provided the following data: m/z(experimental): 632.0147 m/z(calculated): 631.9982

Answer 42

Svar: 26.11 ((632.0147-631.9982) / 631.9982) * 10^6

Question 43

The ionization of peptides performed by ESI generally provides multiple charged peptides Muligheder: Sandt Falsk

Answer 43

Svar: Sandt

Question 44

A triply charged ion (M+3H)3+ is detected at m/z 794.693 (monoisotopic mass). Calculate the molecular mass of the analyte (3 decimals required).

Answer 44

Svar: 2381.056 794.693 = (M + 3*1.007825) / 3 Solve for M, det er så lig 2381.056

Question 45

The intensity of ions present in a mass spectrum correlates to the concentration of the particular analyte in the sample. Mulifheder: Sandt Falsk

Answer 45

Svar: Falsk

Question 46

A mass spectrometer can provide a resolution of R=5000. Select the ion pairs below that may be separated by using this instrument (multiple answers allowed). Muligheder: a) 821.2545 and 821.2571 b) 794.1111 and 794.1233 c) 1438.2437 and 1438.7444 d) 673.1526 and 673.9621 e) 333.5702 and 333.5762

Answer 46

Svar: c og d Vi skal bruge formlen for masseopløsning (R): R = m/Δm Hvor: m = m/z (middelværdi af de to ioner) Δm = forskel i masse mellem ionerne R = 5000 (givet) Der vises to eksempler en som ikke er rigtig og en som er: a) Δm = 821.2571-821.2545 = 0.0026 m = (821.2571+821.2545)/2 = 821.2558 m/R = 821.2558 / 5000 = 0.1642 Dermed ses det at 0.0026 < 0.1642, og derfor kan denne ikke separeres c) Δm = 1438.7444-1438.2437 = 0.5007 m = (1438.7444+1438.2437)/2 = 1438.4941 m/R = 1438.4941 / 5000 = 0.2877 Dermed ses det at 0.5007 > 0.2877, og derfor kan denne godt separeres

Question 47

The compound Olympiadane is composed of five interlocked rings that resemble olympic rings. It's sum formula is C228H236F72N12O30P12. What is the relative mass error if the monoisotopic mass of olympiadane was measured on a mass spectrometer at 5361.421 m/z? (use appendix "Exact masses (Da) of the elements and their isotopic abundances") - Fluorine is missing the table, use the data for fluor from the below table (fluorine only has a single stable isotope): Jeg har valgt at indsætte de værdier der giver mening fra appendixet. Line 1: Name Line 2: Symbol Line 3: Mass Line 4: Abundance Fluorine, F(19), 18.998403, 100 Carbon, C(12), 12.0000, 98.90 Carbon, C(13), 13.003355, 1.10 Hydrogen, H(1), 1.007825, 99.99 Hydrogen, H(2), 2.014102, 0.015 Nitrogen, N(14), 14.003074, 99.63 Nitrogen, N(15), 15.000109, 0.37 Oxygen, O(16), 15.994915, 99.76 Oxygen, O(17), 16.999131, 0.038 Oxygen, O(18), 17.999159, 0.20 Svarmuligheder: a) 1.77 Da b) 2.01 ppm c) 1.37 ppm d) 22.34 ppm e) 1.67 ppm f) 0 ppm g) 1.47 ppm h) 1.57 ppm

Answer 47

Svar: d Bonus info: Man skal tage mass for den der har den højeste abundance af hvert molekyle, og så gange med antallet af det molekyle. Dette skal gøres for alle molekylerne, og så skal dette lægges sammen. Vi kan nu finde masse forskellen i Da, ved at trække den teoretiske værdi fra den målte værdi. For at få det i ppm, skal man nu bruge formlen: ppm = (masse forskel i Da/teoretisk masse i Da)*10^6

Question 48

ESI can produce multiple charge states of the same analyte that may be present in the same mass spectrum. Grouping together the different charge states of the same analyte is called? a) Charge Repulsion b) Centroiding c) Ionization efficiency d) Charge State desorption e) Charge deconvolution f) Isotope Pattern deconvolution

Answer 48

Svar: e

Question 49

The presence of bromine, chlorine or sulphur has an impact on which elements in an isotopic cluster of an analyte? a) The M+1 elements (i.e. M+1,M+2, M+3,....) b) The M+4 elements (i.e. M+4, M+8, M+12,....) c) The M+3 elements (M+3, M+6, M+9,....) d) The M+2 elements (i.e. M+2, M+4, M+6,....)

Answer 49

Svar: d

Question 50

Which of the following events occuring in the ion source have an impact on the mass accuracy in MALDI? a) different initial kinetic energies of ions from the same population b) different starting times of ions of the same population c) different charge states of ions of the same population d) different m/z separation in the mass analyzer e) different matrix f) different starting locations of ions of the same population

Answer 50

Svar: a, b og f

Question 51

Atomic mass can reported both the unit "u" and the unit "Da". a) True b) False

Answer 51

Svar: a

Question 52

For analyzing proteins ___1___, is an appropriate ionization mechanism. Typically proteins are digested into peptides and separated on a ___2___, prior to ___3___ and subsequent introduction into the mass spectrometer. Valgmuligheder: a) ESI b) GC c) EI d) FAB e) qTOF f) liquid chromatograph g) ionisation h) deconvolution i) Fragmenting

Answer 52

Svar 1: a Svar 2: f Svar 3: g

Question 53

What does the "Nitrogen rule" state?

Answer 53

Fra chatten: The nitrogen rule states that a compound with an odd nominal molecular mass contains an odd number of nitrogen atoms, while a compound with an even nominal mass contains either zero or an even number of nitrogen atoms. This rule is based on the fact that nitrogen has an odd atomic mass and forms three bonds, which affects the overall parity of the molecular mass. It applies to neutral organic molecules using the most common isotopes and is useful for interpreting mass spectrometry data and deducing the presence of nitrogen atoms in a compound.

Question 54

What is nominal mass

Answer 54

Nominal mass is the sum of the mass numbers (whole numbers) of the most abundant isotopes of all the atoms in a molecule. It is an integer value that gives a simplified estimate of molecular mass, commonly used in mass spectrometry. For example, the nominal mass of CH₄ is 12 (for carbon) + 4×1 (for hydrogen) = 16.

Question 55

What is average mass

Answer 55

Average mass is the weighted average of the atomic masses of all naturally occurring isotopes of each element in a molecule. It reflects the real distribution of isotopes found in nature and is the value shown on the periodic table. This mass is used when calculating molar mass in general chemistry. Så for carbon ville dette være: (12.00000×0.989)+(13.00335×0.011)≈ 12.011 u

Question 56

what is monoisotopic mass?

Answer 56

Monoisotopic mass is the exact mass of a molecule calculated using only the most abundant isotope of each element. It includes all decimal places and is especially important in high-resolution mass spectrometry because it allows for precise identification of molecular formulas.

Question 57

What is the most accurately defined mass definition that we have? a) Isotope mass b) Average mass c) Nominal mass d) Nominal mass e) Monoisotopic mass f) m/z

Answer 57

E)

Question 58

Which of the following entries are ionization methods in mass spectrometry? a) MALDI b) FAB c) Farraday cup d) EI e) TOF f) ESI g) CEM h) Orbitrap i) qTOF j) CI

Answer 58

Svar: a, b, d, f og j

Question 59

Resolution is synonymous with resolving power (i.e. you may use both terms interchangeably). a) True b) False

Answer 59

Svar: a = True

Question 60

Calculate the nominal mass of the polycyclic hydrocarbon prismane (C6H6).

Answer 60

78 6 * 12+6 * 1

Question 61

Calculate the average mass for prismane (C6H6) (report result with 4 decimals accuracy).

Answer 61

78.1134 6 * 12.0110 + 6 * 1.0078

Question 62

For prismane (C6H6) calculate the monositopic mass. Report result with 4 decimals accuracy.

Answer 62

78.0468 6 * 12 + 6 * 1.0078

Question 63

Formel for mass accuracy in ppm

Answer 63

Mass accuracy (ppm)=(|measured mass − theoretical mass|) / theoretical mass × 10^6 Note: tælleren er i nummerisk tegn og det er monoisotopic mass man skal bruge som den teoretiske værdi

Question 64

What is the basic principle of mass spectrometry?

Answer 64

Mass spectrometry works by ionizing molecules, separating the resulting ions based on their mass-to-charge ratio, and detecting them to determine molecular weight and structural information.

Question 65

Is mass spectrometry inherently quantitative (i.e. does it natively provide absolute abundance?)? Explain why/why not.

Answer 65

No, mass spectrometry is not inherently quantitative and does not natively provide absolute abundances. This is because the signal intensity in a mass spectrum depends not only on how much of a compound is present, but also on how efficiently it ionizes, how it travels through the instrument, and how well it is detected. Different compounds can produce very different signals even at the same concentration due to differences in ionization efficiency, matrix effects, and instrumental response. Therefore, mass spectrometry requires calibration with known standards to accurately quantify absolute amounts.

Question 66

Is electron ionization good for large molecules (peptides, proteins). Explain why/why not?

Answer 66

No, electron ionization (EI) is not suitable for large molecules because it is a high-energy method that causes extensive fragmentation. Large, fragile molecules like peptides and proteins often break apart completely, making it difficult to detect the intact molecular ion.

Question 67

When measuring an analyte with mass spectrometry, the response measured is proportional to the amount of sample applied. Why does the response not directly reflect abundance?

Answer 67

Although the response in mass spectrometry is proportional to the amount of sample, it does not directly reflect true abundance because several factors influence the signal beyond just how much of the analyte is present. Most importantly, different compounds have different ionization efficiencies — meaning some molecules ionize more easily than others under the same conditions. Additionally, matrix effects, instrumental biases, and losses during sample introduction (e.g., ion suppression in ESI) can alter the response. As a result, the intensity of the signal does not correspond exactly to how much of the compound was originally present, unless the system is carefully calibrated with known standards.

Question 68

In mass spectrometry controlled fragmentation is often used to determine the identity of analytes. Is uncontrolled fragmentation a problem, and if so why? Give a short explanation.

Answer 68

Yes, uncontrolled fragmentation is a problem in mass spectrometry because it can produce too many random or overlapping fragment ions, making the spectrum complex and difficult to interpret. It can obscure key structural information, reduce the intensity of the molecular ion (M⁺), and prevent accurate identification of the analyte. Controlled fragmentation, on the other hand, generates predictable and informative patterns that help determine the structure or sequence of the compound.

Question 69

How is isotope pattern deconvolution done?

Answer 69

Isotope pattern deconvolution is done by using mathematical modeling to separate and assign the observed isotope peaks in a mass spectrum to the most likely elemental compositions or molecular species. Here's a simplified overview of how it works:

Question 70

Why do mass spectrometers operate under vacuum?

Answer 70

To prevent ions from colliding with air molecules, which could scatter or neutralize them, reducing sensitivity and resolution. Vacuum ensures accurate ion travel from source to detector.

Question 71

Briefly describe how MALDI works.

Answer 71

MALDI (Matrix-Assisted Laser Desorption/Ionization) uses a laser to excite a matrix that absorbs energy and transfers it to the analyte, causing gentle ionization of large molecules like peptides or proteins without fragmentation. MALDI mainly produces singly charged molecular ions ([M + H]⁺) with little or no fragmentation, making it ideal for determining molecular weights of large biomolecules.

Question 71

Calculate the the mass of the [M+2H]^2+ ion of the peptide NKILKDIIV. Report results with 1 decimals accuracy (use appendix with exact massis of amino acid residues).

Answer 71

528.3 Læg alle residue masses fra peptidet sammen, læg så massen af et vandmolekyle til. Da det er [M+2H]^2+, skal vi lægge yderligere 2 hydrogener til, resultatet af dette skal så divideres med 2, fordi ladningen er 2.