MS Basics

Question 1

Name 5 Major application areas of MS (Ranked)

Answer 1

1. Proteomics (protein identification, quantification, biomarker discovery)
2. Metabolomics & Lipidomics (Small molecule profiling)
3. Small molecules (Drug discovery, food chemistry, environmental science)
4. Synthetic Polymers & Material Science
5. Oligonucleotides & Nucleic Acids
6. (Bio)pharmaceuticals

Question 2

Name the 5 key steps in Mass Spectrometry (SIMDD)

Answer 2

1. Sample Introduction (liquid of gas phase inlet)
2. Ionisation (sample into charged molecular ions)
3. Mass Analysis (separate ions on their m/z)
4. Detection (recording of spectrum: separation & abundance of ions)
5. Data Analysis (interpretation

Question 3

Name the 5 key components of a Mass Spectrometer

Answer 3

1. Ionisation Source
2. Mass Analyser
3. Detector
4. Vacuum System
5. Data Processing system

Question 4

Define Mass Spectrometry

Answer 4

A technique used to identify and quantify the chemical composition of a sample. Get the molecular weight, elemental composition and structural information of the molecules present in a sample

Question 5

What 3 levels of information does MS offer?

Answer 5

1. Molecular weight
2. Elemental composition
3. Structural information

Question 6

Name the two main ionisation types in MS, name 2 common techniques and for what compounds they are relevant

Answer 6

1. Gas-Phase Ionisation –> EI & CI –> for volatile & thermally stable compounds
2. Desorption-Phase Ionisation –> MALDI & ESI –> for non-volatile and thermally unstable compounds

Question 7

Name the Process, Applications and Features of EI

Answer 7

P: High energy electrons collide with vaporised molecules
A: Small volatile compounds (pollutants, drugs) –> GC-MS
F: Extensive fragmentation, structural elucidation

Question 8

Name the Process, Applications and Features of CI

Answer 8

P: Ions generated from reagent gas collide with analytes
A: Small molecules (fragile drugs), less fragmentation than EI
F: Softer ionization, better for molecular ion detection

Question 9

Name the Process, Applications and Features of ESI

Answer 9

P: Ionisation of molecules in liquid phase (LC-MS)
A: Polar, large biomolecules (proteins, peptides)
F: Minimal fragmentation, multiple charged ions, large bio molecules

Question 10

Name the Process, Applications and Features of MALDI

Answer 10

P: Laser strikes matrix-embedded sample, ionising the analyte
A: Large, non-volatile molecules (proteins, polymers)
F: Minimal fragmentation, ideal for mass measurement of large analytes

Question 11

Name 5 Mass analysers

Answer 11

1. Time of FLight
2. Single/Triple Quadrupole
3. Ion trap
4. Orbitrap
5. Fourier-transform ion cyclotron resonance (FTICR)

Question 12

Explain where the ‘charge’ is in Newton’s second law of motion (F = m*a)

Answer 12

‘The charge is hidden behind the F’: because the force exerted by the magnetic and electric field is directly proportional to the charge.

Question 13

Name and explain the two types of detectors used in MS

Answer 13

1. Electron multiplier / Microchannel plate: Amplifiies the signal: ion hits surface –> ejects electron –> electron cascade –> amplification of signal
2. Image detection: non destructive detection of image currents: Ions move near detector –> electrical currents –> frequency reflects m/z –> Fourier Transform frequency to mass spectrum

Question 14

Give the difference between q and z

Answer 14

q is the absolute charge in coulombs
z is the unit charge where z= q/e (e=1.6*10^-19C) –> number of electrons/protons lost

Question 14

Definde a Da

Answer 14

1Da = 1/12 of 12C = 1.66*10^-27 kg

Question 15

Explain the principle of Acceleration of ions

Answer 15

1/2 mv^2= qV
By using an electric field ions are accelerated through a potential difference

Question 16

In what 6 ways can an ion be manipulated with an Electric and Magnetic field?

Answer 16

Accelerate, deflect, trap, detect, fragment, react

Question 17

Explain the principle of Deflection of ions

Answer 17

F = qvB = (mv^2)/r
By using a magnetic and electric field, the ions are subjected to a perpendicular force on its velocity which induces a circular trajectory, with a radius r.

Question 18

Describe Mass Accuracy and Precision

Answer 18

Mass Accuracy refers to how close the measured mass is to the true mass of an ion

Mass Precision describes the reproducibility of the mass measurements (how often the repeated measurement reaches the same value)

Question 19

Describe Mass Resolution and its formula

Answer 19

Mass Resolution describes the ability of a mass spectrometer to distinguish between ions with similar m/z values.
R = M/deltaM

Question 20

Why are isotopes important for MS?

Answer 20

Isotopes are elements with a different mass due to a different number of neutrons. This leads to isotopic distribution patterns specific to elements. This is useful for compound identification and elemental composition information

Question 21

Describe the 3 types of chromatograms you can obtain

Answer 21

Total Ion current (TIC) –> summed intensity across the entire range of masses being detected at every point in the analysis
Base Peak Chromatogram (BPC) –> Displays only the most abundant peak in each spectrum detected at every point in the analysis
Extracted Ion Chromatogram (XIC) –> Signal intensity of specific m/z across the entire spectrum

Question 22

Describe the basics of what you see in a Mass Spectrum

Answer 22

X-axis = m/z range
Y-axis = intensity
Base peak = largest peak in the spectrum/most intense ion
Molecular ion = intact molecule
Noise = random fluctuation that limits detection sensitivity
Baseline = defines background signal level

Question 23

Explain Signal Averaging

Answer 23

Improves signal to noise ratio by Squareroot of n, reducing random noise

Question 24

Why must a mass spectrometer operate under vacuum?

Answer 24

To allow ions to travel freely without colliding with gas molecules

Question 25

Explain the difference between resolution and resolving power.

Answer 25

Resolution measures the ability to separate two ions with a small mass difference, typically expressed as m/Δm, where Δm is the peak width at a specified height. Resolving power is similar but focuses on the ability to distinguish two peaks at a defined mass.

Question 26

Why is MALDI good for analysing large biomolecules?

Answer 26

Fewer in-source fragmentation events

Question 27

What does the peak width at half height represent in a mass spectrometry signal?

Answer 27

2 standard deviations

Question 28

Why is calibration important?

Answer 28

Ensure accurate mass measurement

Question 29

How does the presence of halogens affect the isotopic distribution of a compound?

Answer 29

Halogens, like chlorine and bromine, have distinct isotopic distributions due to the presence of two or more abundant isotopes. This results in characteristic patterns in the mass spectrum, making it easier to identify halogenated compounds.