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Mass Spectrometry Flashcards

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1
Q

What are the 3 core components of a mass spectrometer?

A
  1. Ion source, 2. Mass analyzer, 3. Detector
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2
Q

Why must samples be ionized in MS?

A

The mass spectrometer uses electromagnetic fields to accelerate the ions. This will not occur if the species are neural/noncharged.

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3
Q

What is the function of the ion source?

A

The ion source ionizes samples entering the MS so they can move through the machine which uses electromagnetic fields to move things around. Neutral species won’t work, so the ion source is essential.

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4
Q

A pulsed laser and spotted metal plate are associated with which MS component and of what type?

A

Ion Source - Matrix-Associated Laser Desorption/Ionization (MALDI)

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5
Q

Which ionization technique is shown here? (IMAGE)

A

Matrix-Associated Laser Desorption/Ionization (MALDI)

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6
Q

In the context of proteomics, what is the purpose/application of mass spectrometry?

A

To identify proteins in a sample and characterize their abundance.

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7
Q

Are all ions used in MS cations?

A

Usually, but not necessarily. Although both anions and cations can be detected by MS, positive/cations are almost universally used because removing valence electrons or adding protons is easier

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8
Q

Why does the ion source almost always add positive charge and make cations, rather than anions?

A

Because removing valence electrons or adding protons (making the ion positive) is easier and less energetically expensive than adding electrons (making the ion negative)

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9
Q

What is a hybrid mass spectrometer?

A

A mass spectrometer with a combination of more than one mass analyzer - for example, a quadrupole and an orbitrap.

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10
Q

Why might you want to pair an orbitrap and quadrupole mass analyzer in a hybrid mass spectrometer?

A

While quadrupoles have low mass accuracy and resolving power, they are a very effective component of tandem MS (MS/MS) due to their sieve-like filtering capabilities. Orbitrap is the opposite, with high mass accuracy and resolving power. A hybrid MS with both combines the best traits of the two and makes up for their deficiencies.

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11
Q

What is the main selling point of tandem mass spectrometry (MS/MS)? What does it improve?

A

Resolution is improved in MS/MS through the stacked/multiple rounds of ion separation. It is like running through two sieves - first a larger one, then a fine one.

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12
Q

Describe the steps of an MS/MS run in a QToF mass spectrometer

A

Ions travel from the ion source into the quadrupole where they are separated based on their m/z (1st separation), with only ions of a certain m/z making it through to the ToF mass analyzer where they are propelled and separated by their m/z as they fly toward a detector (2nd separation).

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13
Q

What is this? What does it do? (Orbitrap image)

A

Orbitrap – Current applied to a central spindle causes ions to oscillate around the spindle and side to side. Patterns of oscillation depend on the ion’s m/z and induce current on metal ‘image current plates’ on the sides of the orbitrap chamber as they pass by - a signal that can be read

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14
Q

What is this? What does it do? (Quadrupole image)

A

Quadrupole – Positive or negative DC voltage is applied to four rods (2 positive across from each other, and 2 negative across from each other), producing an electrodynamic field that affects ion motion/movement, allowing you to select for only ions of a particular m/z

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15
Q

What is pictured in the diagram? What is the benefit of this technique? (Reflectron)

A

A reflectron is a retarding electric field that functions as an “ion mirror” in the mass analyzer, redirecting ions around a curve/corner to correct for some of the technical variation that can arise from slightly uneven ionization times or locations

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16
Q

Which has a higher resolution, A or B? (image) What does this say about the mass accuracy?

A

B has the higher resolution because it is able to distinguish 3 peaks where A blends the 3 into 1 peak. This does not say anything about the mass accuracy. Just because there is high resolution, does not mean the information those high-resolution peaks convey is accurate.

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17
Q

What kind of MS is shown? (Image of a hybrid MS with quadrupole and ToF combined with a reflectron)

A

A hybrid mass spectrometer featuring a quadrupole to separate ions by m/z, then a collision cell to fragment ions by nitrogen bombardment, a pusher to release ions all at the same time into the ToF, a reflectron to correct for any technical noise, and a detector to read the m/z signal

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18
Q

What are three common types of ion source?

A
  1. Electron/chemical Ionization 2. Matrix-Assisted Laser Desorption/Ionization (MALDI) 3. Electrospray ionization (ESI)
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19
Q

How does MALDI work?

A

MALDI works via a UV laser which is fired through the metal plate onto which samples are spotted, ionizing them off the plate and accelerating them into the mass spectrometer

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20
Q

How does ESI work?

A

ESI works by spraying peptide samples mixed with acidified liquid and organic solvents out of a capillary tube attached to the positive terminal of a high-voltage power supply. The plume repels and when charge density reachest the Rayleigh limit, they propel into the mass analyzer

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21
Q

Rayleigh limit

A

The maximum amount of charge a liquid droplet can carry. At this limit, droplets send out fine jets of liquid.

22
Q

What are the advantages of ESI?

A

ESI is easy to use alongside liquid chromatography and its solution-based environment is more natural for nucleic acids and peptides/proteins

23
Q

MALDI is commonly paired with what type of mass analyzer? Why?

A

MALDI is commonly paired with Time-of-Flight mass analyzers because the laser ionization creates a distinct “start” time for the ToF “race”

24
Q

What is the mass analyzer? What is its function?

A

The mass analyzer is the chamber through which ions move. Its function is to sort and separate ions according to their mass (m) and charge (z).

25
Q

By what rule/principle does the mass analyzer work?

A

Newton’s second law - force is equal to mass times acceleration (F = ma). The mass analyzer separates ions by applying a magnetic or electric force, causing them to accelerate at a speed dependent on their mass.

26
Q

Equation for Newton’s second law

A

Force = mass x acceleration

27
Q

Is the magnetic/electric force applied to ions inside the mass analyzer uniform? How come they accelerate differently?

A

While the force applied is constant, how force affects the ion depends on its charge. Ions of different charge will experience force differently, and therefore will accelerate differently depending on both their charge and mass, even though the force is constant.

28
Q

Mass accuracy

A

How close the experimentally measured mass is to the true mass of the ion

29
Q

Term - how close the experimentally measured mass is to the true mass of the ion

A

Mass accuracy

30
Q

Resolution

A

How well close-together peaks can be measured/separated as distinct entities

31
Q

Term - how well close-together peaks can be measured/separated as distinct entities

A

Resolution

32
Q

Give 3 common types of mass analyzer

A
  1. Time of Flight (ToF) 2. Quadrupole 3. Orbitrap
33
Q

How does a Time-of-Flight mass analyzer work?

A

Ion race: the time it takes for ions to travel from the “start” point (ion source) to the “finish line” (detector) is indicative of their mass

34
Q

In a ToF, would you expect a high or low mass ion to travel faster?

A

Smaller ions travel faster (F = ma –> F/a = m)

35
Q

What are other terms for the ToF?

A

Ion drift chamber or flight chamber

36
Q

Reflectron

A

A retarding electric field that functions as an “ion mirror” to redirect ions around a corner and correct technical variation that results from them ionizing at slightly different timepoints

37
Q

A retarding electric field that functions as an “ion mirror” to redirect ions around a corner and correct technical variation that results from them ionizing at slightly different timepoints

A

Reflectron

38
Q

MALDI uses a laser to ionize samples, but there is a tiny amount of variation - not all samples ionize at exactly the same time. This can cause noise in a ToF. What is one way you might mitigate this technical variation?

A

Addition of a reflectron (image)

39
Q

How does the quadrupole mass analyzer work?

A

Positive or negative DC voltage is applied to four rods (2 negative opposite each other and 2 positive opposite each other), producing an electrodynamic field that affects ion motion/movement, allowing you to select for only ions of a particular m/z by spinning away the undesirables

40
Q

Which mass analyzer is most effective for m/z selection?

A

Quadrupole - electrodynamic field affects ion motion/movement, allowing you to select for only ions of a particular m/z by spinning away the undesirables

41
Q

Con of quadrupoles

A

Low mass accuracy and resolving power

42
Q

Pro of quadrupole

A

Electrodynamic field allows you to select for specific m/z ranges

43
Q

What is a triple quadrupole?

A

Sequential stacking of quadrupoles to layer m/z selection and refine sample –> extremely accurate quantification

44
Q

SRM, MRM, and product ion scans are all what type of MS?

A

Triple quadrupole

45
Q

How does the orbitrap mass analyzer work?

A

A current is applied to a spindle which rotates, causing ions to oscillate around it as well as side to side. The pattern of oscillation depends on their m/z, which can be read by image current plates as ions pass them

46
Q

Image current plate

A

Metal plates in the orbitrap chamber that read ion charge as ions pass by them

47
Q

Metal plates in the orbitrap chamber that read ion charge as ions pass by them

A

Image current plate

48
Q

What type of hybrid MS is common in proteomics and why?

A

Tandem quadrupole ion trap MS/MS is very high throughput and therefore popular in proteomics

49
Q

What are 3 common types of detectors?

A
  1. Electron multiplier 2. Faraday cups (FC) 3. Ion-to-photon
50
Q

What is pictured in the diagram? Why is there so much black on the right? (Electron multiplier dynode)

A

An electron multiplier dynode which amplifies current many times over as electrons are ejected in a cascade, as shown in black.

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