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Summary Mass Spectrometry

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This is a summary of the course Mass Spectrometry given in 2022 at the UvA. I summarized all the lectures by using the slides of the presentation, the professors and added information from the internet for hard subjects. This year is a closed book exam.

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  • 14 december 2022
  • 63
  • 2022/2023
  • Samenvatting
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jeanine0413
Summary Mass Spectrometry

By Jeanine Koelewijn – 2022

,Inhoudsopgave
Les 1: Mass spectrometry principles – Gary ...................................................................................................... 3
1.1 Intro mass spectrometry ............................................................................................................................... 3
1.2 What’s in a mass spec .................................................................................................................................. 5

Les 2: Electron and Chemical ionization ............................................................................................................ 8
2.1 Electron Ionization (EI).................................................................................................................................. 9
2.2 The molecular ion ....................................................................................................................................... 12
2.3 Isotope peaks .............................................................................................................................................. 12
2.4 Chemical Ionization (CI) .............................................................................................................................. 14

Les 3: MALDI and TOF..................................................................................................................................... 17
3.1 MALDI ......................................................................................................................................................... 18
3.2ToF – Time Of Flight..................................................................................................................................... 19
3.3 MALDI – MS imaging .................................................................................................................................. 21

Les 4: ESI, ion traps, quads ............................................................................................................................. 22
4.1 ESI – electrospray ionization ....................................................................................................................... 22
4.2 Iontraps ...................................................................................................................................................... 25
4.3 Quadrupoles ............................................................................................................................................... 27

Les 5: Scanning modes, protein identification, hybrid analysers..................................................................... 29
5.1 Scanning modes.......................................................................................................................................... 29
5.2 Protein Identification by MS ....................................................................................................................... 32
5.3 Hybrid Analysers ......................................................................................................................................... 34

Les 6: Fragmentation ...................................................................................................................................... 38

Les 7: LCMS – hyphenation ............................................................................................................................. 44

Les 8: Orbitrap & Ambient MS ........................................................................................................................ 49
8.1 Orbitrap ...................................................................................................................................................... 49
8.2 Ambient MS – Ambient ionization .............................................................................................................. 51

Les 9: Protein identification & Quantitation ................................................................................................... 56
9.1 Quantitative proteomics ............................................................................................................................ 56
9.2 Protein identification .................................................................................................................................. 59

Les 10: MS in life science ................................................................................................................................ 61




2

,Samenvatting -- Mass Spectrometry 2022/2023
Jeanine Koelewijn


Les 1: Mass spectrometry principles – Gary

1.1 Intro mass spectrometry

What is mass spectrometry
- Mass spectrometry is an analytical tool useful for measuring the mass-to-charge ratio
(m/z) of one or more molecules present in a sample
- These measurements can often be used to calculate the exact molecular weight of
the sample components as well

MOST often used for:
• Identify via molecular weight determination (match to known mass)
• To quantify known compounds
• Determine structure and chemical properties of molecules

HOW:




we get multiple levels of information
1. Molecular weight → molecular mass
2. Elemental composition → isotope pattern of atoms in molecules
3. Structural information → tandem mass spectrometry

IONISATION

Gas phase (for these the compounds need to be naturally volatile and thermally stable)
- Electron (EI)
- Chemical (CI)

Desorption phase (when the compounds are non-volatile and thermally non-stable)
- Electrospray (ESI)
- Matrix assisted laser desorption/ionization (MALDI)

MASS ANALYSERS
- Time of flight (TOF)
- Double focusing
- Quadrupoles (Q)
- Iontrap (IT)
- Fourier-transform ion cyclotron resonance (FTICR)



3

, - Orbitrap (Orbi)
- Qtof
- QIT/ORbi

All work on the same principle of ion movement and manipulation

F=m*a

F: magnetic or electric field to exert a force on an ion
a: this force accelerates ions differently
m: depending on the mass of the ion


Grams are not a good unit of mass for something this small

1 Da = 1.660538921 x 10-27 kg

1 Da = one twelfth (1/12) of the mass of an unbound neutral atom of carbon 12

The analyte must be charged (an ion)!
- We always measure m/q or m/z
- Mass of an ion differs from that of a neutral

q = -+ ze

q = the absolute/electric charge on an ion (SI unit:coulombs)
z = the unit charge (where q = z x e , the number of electrons/protons gained or lost, 1 2 3 4)


acceleration of ions VS deflection of ions

Acceleration:
Consider an ion of mass m and charge, q, in a potential difference of V.
The ion will accelerate through the potential gaining velocity.

The kinetic energy gained (1/2 mv2) = potential energy (qV)




4

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