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Chem Bio > Mass Spec mid term > Flashcards

Mass Spec mid term Flashcards

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1
Q

Why would we want to change the end product of the CI I/M reactions of the reagent gas?

A

For our analyte to ionize, the reaction needs to be exothermic (at least 2 kcal/mol - or else too slow) so changing what is interacting with our analyte will change Delta H (moderate means can see M+H, but if we want to fragment - can tune for a reagent that gives a larger delta H).

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2
Q

How to tune for different reagent end products in CI?

A

Change pressure (change the amount of collisions - changes which reactions more likely)

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3
Q

Nitrogen Rule

A

The nitrogen rule states that any molecule (with all paired electrons) that contains an odd number of nitrogen atoms will have an odd nominal mass.

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4
Q

What is mean free path dependant on

A

Collisional Cross section and density of neutrals (also temp and radii)

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5
Q

Sack rule for Mean free path

A

4.95/pressure (mtorr) (give MFP in cm)

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6
Q

What is mass defect and how does it play into monoisotopic mass?

A

The equivalent of the energy of binding (and from e = mc^2 we know this has a mass that adds to our analyte)
So when we talk about our exact mass of isotopes – it’s not just the sum of proton , neutron electron etc its that + mass defect (EVERY ISOTOPE HAS UNIQUE MASS DEFECT)

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7
Q

Resolving power formulas

A

IUPAC – M/Delta M – M is mass we’re at and delta M is the difference between two adjacent peaks at equal abundance with a specific overlap defined (50%)
Common(?) – Full Width Half Mass (FWHM) at a specific x hiegh at a specific M

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8
Q

Mass accuracy formula

A

(Mexp -Mcalc)/Mcalc (exp is experimental, calc is true)
Expressed in terms of PPM – (multiply by 1 million)

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9
Q

What is efficiency

A

16) EFFICIENCY – product of transmission of analyzer and duty cycle
a. Duty cycle - % of ions of INTEREST ionized
-measurement dependant (SIM high duty cycle, scan - low)

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10
Q

List operating pressures for the following:
EI, CI,

A

10^-5 for EI, 0.1-0.5 for CI

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11
Q

Pressure regimes

A

Low - <10^-5 (most everything else); Moderate 10^-5 – 10torr (CI) ; > 10 torr (AP)

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12
Q

4 ionization mechs for EI

A

1) gets hit - M+ dot
2) Gets hit - fragments
3)gets hit loses multiple electrons (M n+)
4) Picks up electrons (M- dot)

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13
Q

What is ionization cross section

A

is a measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon. - it’s dependant on pi * b (impact parameter)

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14
Q

How does ionization occur in EI

A

The wavelength of the electron is close to molecule bond length – the wave becomes disturbed
-if one of the frequencies has an energy matching a transition in the molecule – energy transfer occurs – which can lead to electronic excitation and if this has enough energy (Ionization potential) – an electron can be expelled

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15
Q

Draw the mclafferty rearrangment

A

look it up

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16
Q

What are the pressures of the CI parts

A

sample is at 10^-5 , reagent gas is at 0.1 ish analyzer at 10^-5 so there’s a lot more reagent than sample

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17
Q

What exothermicity does our reaction need to be at and why for CI?

A

2 kcal/mol at least - otherwise reaction too slow

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18
Q

What are the units of kcoll

A

in solution its: 1/Ms (in gas phase its cm^3 / molecule *s

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19
Q

For a CI reaction (given our rate equation) what is it dependant on

A

N and T

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20
Q

What determines fragmentation in CI

A

internal energy distribution, observational window, collisional cooling (pressure)

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21
Q

How does electron energy compare from CI to EI

A

Higher to get through the many more neutral molecules

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22
Q

Alternative reaction can see in CI

A

Adducts, e- transfer, hydride extraction, cluster formation, e- capture (negative), metal ion attachment

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23
Q

EI vs CI in terms of ionization

A

Soft vs hard
-ability to generate negative ions for CI
-DIFFERENT FRAGMENTATION PATHS due to odd vs even electron species being formed
Can tune CI reagent gas
-M+H
-less fragmentation pathways – more predictable
-ionization flexibility – can pick types of ions you want and pathway H transfer, e- transfer, adducts etc

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24
Q

steps in apci

A

liquid goes through - nebulized -heated for vaporization- corona discharge to ionize via chemical ionization so most of the initial ions are the solvent

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25
Q

Examples of spray ionization techniques

A

ESI 1uL/min flow rate), Ion spray (1 mL/min flow rate (or less) - ,
SONIC SPRAY – (can make both polarity ions ) – little to no voltage,
ULTRA SPRAY – (less than .5 uL /min flow) – also uses ultrasonic vibrations,
THERMOSPRAY - .1 mL/min flow rate,
NANOSPRAY – nL/min flow rate – lower voltage than ESI -no assisting nebulization

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26
Q

Benefits of ESI

A

From solution, good for proteins, multiply charged, can do soft ionization, LC

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27
Q

Important parameters in onset voltage

A

Major are solvent surface tension (+corr) and radius of capillary (- corr), a

lso includes capillary to counter electrode distance (positive correlation), permitvity of vacuum (- cor)

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28
Q

What is electric field at emitter based on and what does this mean for nESI

A

+ corr: voltage, - corr: capillary radius and Distance. Means since smaller cap radius and distance - need less voltage for same field

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29
Q

draw an ESI source with the electrodes

A
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30
Q

How do you increase the electrochemical effects in ESI

A

non buffered solution, lower flow rate, high oxidation potential metal contact and NESI

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31
Q

What determines what gets oxidized in ESI

A

Current of ions striking the counter electrode

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32
Q

What is the ion current based on

A

Flow rate, conductivity and electric field

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33
Q

3 models of ion formation in ESI and differences

A

1) Ion evaporation (small molecules in progeny droplets) 2) Charge REsidue (larger proteins,wait until all solvent evap) 3) Chain ejection (denatured proteins - eject one residue at a time)

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34
Q

What are ways to deal with cold ions (create clusters)

A

Accelerate with electric field (potential issue with in source frag), Heat the capillary they’re coming from, use a curtain gas to heat them

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35
Q

What does a bimodal distribution mean in our spectra

A

A different protein conformation

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36
Q

What are things that control what we see in the spectra for ESI

A

pH , e chem reactions, what species are on the surface of a droplet, I/M reactions, basic strength of solvent, in source fragmentation, and droplet evaporations (earlier , later , last concentration etc)

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37
Q

charge state deconvolution formula

A

N = (m2-1)/(m2-m1)

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38
Q

NOTABLE ESI FOM

A

linear dynamic range - not as stable, subject to matrix effects, multiply charging, subject to non volatile salts, clogging etc.

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39
Q

Examples of ambient ionization

A

DART (electric discharge plasma. produce ions , electrons and excited state species), DESI (ESI at surface), REIMS (AC electrical current to aerosolize)

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40
Q

What is Field Desorption/Ionization and what are the differences

A

FI - voltage applied to a filament (carbon dendritic tip) positive voltage at tip - causes electron tunnel from molecule to the wire and there resulting ion is repelled. In DI - wire is coated with sample - current applied and sample desorbed (also heats it up) POTENTIAL COMES FROM TIP TO A CATHODE.

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41
Q

How does SECONDARY ION MS work

A
  • Primary ion beam (keV, ar+, Cs+) sputters a whole host of species from surface – in the plume (selvedge) lots of interactions (these come largery from the surrounding region not the direct hit (also small molecules closet to impact, proteins and larger farther away
  • Unique because can do dynamic sims and get top few layers (as opposed to STATIC SIMS)
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42
Q

Fast atom bombardment - what is it, how does it work, big ideas

A

uses kEV (Xe, argon) - ions formed then accelerated then neutralized before collision

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43
Q

What is FAB good for

A

biologicals, positives and negatives of the same intensity

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44
Q

What is FD/FI used for

A

soft ionization, large MW, non polars (polymers)

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45
Q

Liquid SIMS vs normal SIMS

A

uses a matrix - such as glycerol - allows for I/M reactions - can refresh surface (longer lasting signal)

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46
Q

Matrix selection in liquid SIMS

A

unreactive, absorb E, no background signal, transfer E to anlayte, vacuum compatible

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47
Q

What do DI and Ionization in laser desroption ionization depend on

A

Wavelength, power, pulsed vs continuous
- mw - only useful for <1000 m/z – too much frag

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48
Q

MALDI MODELS of ionization

A

Lucky Survivor - essentially saying in the selvedge region - most ions preformed and get neutralized there and we only see those that don’t get neutralized
Photo excitation and Pooling - -2 matrix molecules – raised to first singlet state (S1) – and are close and experiencing stacking interactions – energy pooling can occur – typiacally need 2x (2-3 photons for ionization

Direct multiphoton ionization: direct hit by photon to remove electron - not likely due to speed

Excited state Proton transfer: When matrix molecule gets excited - becomes more acidic - donates a proton (not likely

Pneumatic assistance/pressure pulse: low MW gaseous fragments of matrix (generated by thermal decomposition ) - provide the mechanical force for disintegration (not likely given matrixes don’t often thermally decompose)

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49
Q

STEPS OF MALDI

A

Fire laser - matrix absorbs energy converts to heat -cause sample to disintegrate - go into gas phase -selvedge region where variety of interactions (matrix - analyte charge transfer reactions reaching thermal equillibrium

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50
Q

What does a MALDI spectra reflect?

A

The thermodynamics of analyte analyte and matrix analyte reaction in the plume (bimolecular ion molecule reactions) proton, e- and cation transfer

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51
Q

THINGS THE MATRIX IN MALDI CONTROLS

A

Frag (hot vs cold),
solid vs liquid ( can refresh surface),
acid vs basic
absorbing wavelength

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52
Q

Describe fragmentation in MALDI

A

Generally soft ionization but can get additional fragments in 2 ways
ISD -in source - radical transfer reactions and subsequent unimolecular dissociation during ionization
PSD - metastable fragmentation after source

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53
Q

How does power affect fragmentation Maldi

A

does not scale with it (scales with material ablated

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54
Q

noable FOM of MALDI

A

a lot of singly charged, can form both polarities, M+H, M-H, abundant chemical noise at low m/z

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55
Q

What determines what is seen MALDI on spectra (matrix wise)

A

pH, composition , acidity and basicity of matrix

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56
Q

Methods for ion transfer

A

nozzle skimmer vs transfer line

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57
Q

What is Space charge, why is it important and what is it dependant on

A

The idea that all our ions being in the same places naturally causes some repulsion and divergence (optics issue)- inverse with radius, velocity, vacuum permittivity and correlates with initial current

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58
Q

Difference between strong and weak focus

A

Strong focus is done with main field lines, weak with fringe field

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59
Q

In electrostatic field - what are ion trajectories based on

A

q*E = 1/2 mv^2

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60
Q

Why is accelerating good in optics

A

It minimizes initial energy spread relatively

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61
Q

What is LIOUSVILLE’s theorem

A

x1a1v1 = x2a2v2 (so basically this is a way we can focus or tune some of these parameters - explains also how accelerating an ion can tighten our x or a

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62
Q

How does an ion lens: change velocity and how does it deflect a beam

A

to chagne velocity it passes it through a different E field (stronger), to deflect - it curves potential contours

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63
Q

Limits on Liousvilles theorem and how we can focus ions

A

Generally theres a max acceptance angle for lenses so can’t mess around with that too much, also acceleration does not correct for positional dist but it does mitigate it

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64
Q

What are the two variations on electrostatic lenses and how do they differ -draw them, some basic facts

A

Thin vs THick -always convergent

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65
Q

2 kinds of electrostatic lenses and what are their differences

A

Einzel and Immersion. Einzel is 3 lenses the 1st and 3rd have the same V so overall no acceleration, Immersion does cause acceleration

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66
Q

Draw how immersion lenses work (accel to deccel and vice versa

A
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67
Q

2 major aberrations in electrostatic elements
and how to fix

A

Chromatic -slower ions are affected greater, (impart large energy on them to fix) and Spherical (field strength can vary by the edges, imperfect electrodes etc) (fix by skimming off edges

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68
Q

magnetic field force

A

evB

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69
Q

Strong focusing equations (basics and what they mean)

A

phi(x,y) = V/(r^2) (x^2 - y^2) With the laplace condition we get 2a + 2b = 0 such that a = - b (why we have these poles at opposites for focusing - so in x if focusing - defocusing in y

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70
Q

How do you focus with only DC quadurpoles

A

You put one DC quadrupole with one orientation (eg x + and y defocus) and then another one right after it in the opposite - and you keep going (ion pipe)

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71
Q

Draw multiple pole devices plots (x position with correcting force and explain why some might be better at better functions

A

look up diagram

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72
Q

What is a brubaker lens

A

A lesns before a DC quadrupole (or anything ) where fringe fields right before have an unwanted effect so Brubaker lenses (similar 4 poles so matches up) are placed before with a fraction of AC current to prevent any interference - creates wider acceptance angle and greater transimission

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73
Q

What is an ion funnel and how does it work

A

A series of electrodes in which the field free region can be calculated by their distance from each other - as you go down it - you decreases this distanceso the ions are pushed into a higher and tighter region
-ALTERNATING out of phase AC with a DC gradient

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74
Q

Equation for drift time in a TOF

A

D/ROOT(2U) * ROOT(m/z) so directly related to D but notably related to ROOT (m/z) - important for resolution

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75
Q

Relation between time and mass in TOF

A

m = t^2 so any difference in time is squared for a difference in mass

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76
Q

Things that affect T in tof

A

v, position and directional spread but also ionization time

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77
Q

Ways to deal with directional spread? (3)

A

use non gaseous source, or accelerate those turned around longer, or increase D so that turn around time is a smaller % of overall

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78
Q

pulse ion extractin - know it

A
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79
Q

Reflectron - what is it and why

A

Series of lens – as ion enters – reach 0 KE and sent the opposite direction with the same KE – good because improves resolution – and corrects for velocity spread

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80
Q

Benefits of orthogonal extraction in TOF

A

Increases efficiency (gives time of fill – continuously use ions- improve duty cycle)
In fill region velocity small relative acceleration (especially in direction of TOF)
Can get collisional cooling in multipole to focus ions and reduce vdist

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81
Q

What connects TOF to TOF in a TOF-TOF instrument

A

an ion (voltage) gate to collect ions from first TOF

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82
Q

Ways of processing pulses in TOF?

A

Digital transient recording vs Ion count
Digital transient reads all the time - takes a lot of memory but can deal better with multiples ions at detector at same time - Ion count only reads when something hits - more efficient can’t deal with isomers as well -increas Rs

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83
Q

What is ADC sample rate

A

analogue to digital conversion -important because literally determines points/scale on our plot - and determines points per peak (changes form a triangle to a peak with detail -increase Rs

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84
Q

FOM for TOF

A

unlimited mass range theoretically (as get bigger go really slow can have issue making a detectable signal), resolution 60k, single digit ppm

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85
Q

PPM for instruments?

A

TOF , FTICR, Sector - single digit ppm
QMF - 10’s of ppm
3d Ion trap - 10’s of (50)

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86
Q

Positional spread in a TOF

A

So we can accelerate differentially - the issue is that these focus at a distance that’s often too short (D= 2SA0 we can increase this with 2 stage acceleration but need to not have v spread

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87
Q

MCP gain

A

1 million

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88
Q

What is the lorentz force right hand rule?

A

Hold hand out - fingers point towards magnetic field, thumb towards ion velocity and palm towards force of mag field (FOR NEGATIVE IONS USE LEFT HAND)

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88
Q

What is the lorentz force right hand rule?

A

Hold hand out - fingers point towards magnetic field, thumb towards ion velocity and palm towards force of mag field (FOR NEGATIVE IONS USE LEFT HAND)

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89
Q

What is m/z related to in sector instruments (and how derived)

A

(r^2B^2)/2U (derived from setting kinetic energy = qU and solving for v and then sub that into qvB. We then set that - to centrifugal force (mv^2/r) and it simplifies to what we have

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90
Q

Given r^2B^2/2U how does a sector instrument scan m/z

A

by varying U or B

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91
Q

in sector instruments r is also proportional to

A

Momentum

92
Q

What are the distributions present and how are they dealt with

A

m/z dist -dealt with by scanning, positional - using narrow slits, angular - it actually focuses, and velocity Need to use an electric sector before hand

93
Q

Fringe field effects on Sectors

A

Can cause the spherical aberrations where those on the outside can be affected differently -so makes a laminar flow type shape - not good because doesn’t match slit- typically deal with by reshaping it with a DC multipole

94
Q

Know how to draw barbers rule

A
95
Q

What is equation for electric sector and how derive?

A

r = 2Ek / (q*U) note Ek and qU are different electric fields ( one is initial acceleration and one is for the electric sector) Obtain this by solving for v (1/2 mv^2 = qU) and then setting our electric sector force = to centrifugal force and substituting in for v and solving for r (note when writing this Ek is just the qU = to the 1/2 mv^2 in the beginning - initial kinetic energy)

96
Q

Because electric sectors dont follow Barbers rule - what are some special cases of moving thee focal points

A

127.17 - focal points at entrance exit
phi -63.6 - focal points are r/ROOT(2) from entrance or exit
phi - 31.8 - exit gives parallel bea,s

97
Q

Different types of gemoetries for forward double focusing secotrs

A

Mattauch-Herzog - point to line
Nier Johnson - point to point

98
Q

What is sector instrument resolution based off of

A

Slit width, V and B (how perfect these fields are), focus of V and angle

99
Q

Resolution vs resolving power

A

resolving power is : m/Delta(M), resolution is just Delta M (delta m can be which can be peak width FWHM or the Delta M at which 2 overlapping peaks have a valley of 10% peak heights

100
Q

What do MIKES tell us about

A

translational energy of the products (KER)-kinetic energy release

101
Q

Calculate dispersion due to mass in a sector instrument

A

So dipsersion for constant B and V is 2dR/R = dM/M so this equals 2dR = R * (dM/M) (this comes from taking the derivative of r^2 proportional to m) and this = Dm or dispersion due to mass (which is not dM) -note dm/M is 1/resolution - so if we’re given an r (eg a radius for our ions) - 30 cm - and we want a resolution of 1000 - we multiply 30cm * 1/1000 - and that gives us our dispersion due to mass (THIS ISN”T DISPERSION IN MASS but dispersion in RADIUS due to mass). This tells us for this resolution what the slits should be smaller than

102
Q

What is the equation that tells us how dispersions in their parameter effect our radius and slit width

A

r^2 = (2mU)/(eB^2)
from this we get the relationships 2dr/r = dm/m
2dr/r = dU/u, and I guess 2dr/r = B/2dB in which we can calculate dispersion due to any of these factors (assuming the other parameters are kept constant)

103
Q

How is sector resolution simplified

A

its simplified to slit width assuming well focused V and angles and that the electric and magnetic fields are stable.

104
Q

What is the sector mass range equation

A

B^2r^2 / (2U (actually the same as our m/z one) - shows you can increase B, or r or decrease U but decreasing U not recommend for resolution

105
Q

Notable FOM for sector instruments

A

accuracy single digit PPm, reoslving 100-100k, poor efficiency, big expensive

106
Q

What are weighting parameters and what are they for common quadrupole MS’s

A

lambda, sigma and gamma - for 2D - QMF and LIT - lambda and -sigma = 1 and gamma = 0
For 3d - they each lambda and sigma = 1 and gamma = -2 (whole thing needs to = 0 - laplace)

107
Q

Have the a and q terms memorized and maybe basic derivtaion of it

A

see notes - maybe for derivation start with F=ma = d(phi)/dx = Phi(x)/ero^2 and that equals ma as we said so it equals m * dx^2/dt^2 so acceleration = phi(x)/(mro^2)

and then phi(x) can be expanded to 2( U + Vcos(ohm)t) which are our DC and RF terms) and we get to a and q by putting it through the Mathieu equation

108
Q

a and q terms?

A

8 eU (a) and - 4eV (q) (and both are over m * r^2 * Ohm^2

109
Q

Describe how quadruple orbit occurs

A

DC pushes it axially and radially has lissajou orbits as the RF and DC potentials alternate causing it to constantly be rolling downhill in different directions (pringle chip

110
Q

Know generally how mass is filtered/selected in QMF

A

as increase q move larger ions up scale (always goes large to small) and can increase DC to push up Mathieu curve

111
Q

Issues with quadrupole and fixes?

A

Imperfect fields from the electrodes and fringe fields. Fringe fields dealt with by Brubaker lens, can be limited with V and power limit to get up to certain values to accommodate certain m/z

112
Q

FOM for quadrupole

A

mass acuraccy - 10’s of ppms, resolving 1-2k, mass range 2-8k,

113
Q

Resolution in quadrupole related to what?

A

oscillation cycle in field so faster ions are resolved better

114
Q

Basics of math for 3d trap

A

so start with same phi/r^2 (dphi/dx +dphi/dy +dphi/dz) except we convert our x and y into radians so just one radial term and one z term - and due to laplace they need to =0 so they equal each other( ro^2 = 2 z^2)

115
Q

3 ways traps are operated

A

phi on ring and - phi on end cap electrodes (mode 1), phi on ring electrode and end cap grounded (mode 2 - common), RFt o ring and DC to endcaps

116
Q

2 major types of movements in the trap

A

The secular frequency and the ripple motion that comes from the drive frequencies when close to the poles

117
Q

What is the Dehmelt approximation

A

ignore ripple motion (q<0.4) and can calculate secular frequency

118
Q

What is the secular frequnecy equtaion (include equation for beta)

A

w = (n + (1/2)B)OHM ( can be negative or positive for negative or positive n)

B= ROOT(a + (q^2)/2)

119
Q

equation for ion trap well

A

Dz = 1/8V*q

120
Q

Explain how the well trapping effects what we can trap at simultaneously and how it relates to the LMCO

A

The well is around certain masses - those near the edges have less holding them in and if they have enough energy can leak out - can adjust q so deeper in well but then potentially those farther away in m/z are no longer trapped (so depending on what your q is at and what m/z are best trapped for - determines your LMCO - won’t be able to trap past a certain range

121
Q

Imperfections in the trap and issues it can cause

A

Since electrodes truncate - there are imperfections in the field and higher order fields at work which alter the relationship mathematically defined between secular frequency and m/z- some are incorporated in such as in the stretched trap to deal with a mass shift error or to alter resolution. can also cause black holes (areas of instability) or enhanced ion heating

122
Q

Ways to store ions and mass analyze

A

1) continuous ionization and mass selective stable scan (a lot messy)
2) pulsed ionization with mass selective stability scan (so only trap 1 m/z at a time and send to detector
3 Pulsed ionization and mass selective instability scan - where ramp V to eject masses in sequence to the detector (rammp up to q = .908) so can get entire spectra with one ionization
4) resonance ejection - like pulsd ionization mass instability scan but you apply a supplemental waveform at which they’re kicked out
4

123
Q

Talk about resonance ejection - some concerns, some pros

A

Need to remove low mass ions that are after the supplemental wave form so no spectral confusion. It is good for resolution as this wave form can apply an octopolar field such that as displaced further from center as we’re doing by ramping RF - THey’re ion frequencies increase even more (greater than our typical r^2) which means as gets closer to ejection -results in a higher frequency and better resolution as ejected faster ( a slower ion with slower frequency means worse resolution), allows to extend mass range by ejecting at an earlier Q (think really big ions - less of a voltage needed to get them to an ejection point)

124
Q

How can supplemental waveforms for resonance ejection be applied

A

Dipolar or quadurpolar - apply your supplemental AC to either two opposing rods or to all 4 at once

125
Q

HOW IS RESOLUTION IN A 3 d ion trap determined

A

Based on time - the more time the more it has to come into resonance with the AC voltage - BUT this comes at a cost of signal (coulombs/s) to deal with - can scn a smaller mass range at a slower time to get better resolution

126
Q

3d ion trap PPM

A

50 ppm, space charge effects - effect how much you can trap,

127
Q

What is APEX isolation

A

how it is done in a QMF by keeping it in the Apex

128
Q

Know how to calculate selected ion ejection (excel sheet slide)

A

may need to ask someone

129
Q

In a sector instrument calculate the allowable change in voltage given a desired resolution and radius and given voltage

A

OK so for this we start with our r^2 = m2U/(qB^2) and FIRST we need to determine the variance in R allowed that makes this resolution (and determines our slit width) we get the relationship r^2 = m (proportional) so derivative 2dr/r = dm/m - we can solve for change in r as r*dm/m (which is r * 1/Rs) and that gives us the allowed variation in radius for that given resolution. SO for voltage - we can make another similar relationship r^2 = U - take derivative 2dr/r = dU/U BUT now we want to solve for dU (the variation in voltage). so that is solved by 2dr/r * U - WE KNOW 2dr because we just solved for it - this is the max variance that we can have for this resolution SO our change in voltage can only cause a variation of that so we sub in and get max allowable change in voltage

130
Q

What is a scan function

A

The various waveforms, rampings , m/z selected for that an ms does for a run

131
Q

How can we extend the mass range of a quadrupole

A

Bigger power supply (increase volage), lower ro, lower frequency, and increase the charge (multiply charged)

132
Q

at high m/z for a quadrupole - what is comproised in terms of FOM

A

Trapping efficiency, scan range, resolution

133
Q

What are other ways to scan a trap besides Q (reasonably used)

A

scan across frequency, scan across A(downscan)

134
Q

Talk about the downscanning in quadurpole and benefits/issues

A

Varies A - and actually lowers it so ions eject on the downward portion of the stability diagram. Issues: the line is curved not straight - so not a linear response needs to be adjusted, also ejecting in reverse (higher m/z first) - can be a benefit but also means spectra reversed typically . The benefits are typically the reverse of issues at high mass range (better resolution, scan speed and trapping efficiency)

135
Q

Which is more efficient LIT or QIT

A

LIT (easier to get ions in and out - harder with QIT but traps better)

136
Q

What are the ways one can do mass analysis in an LIT

A

mass selective radial or axial ejection

137
Q

How does LIT radial ejection work

A

The electrodes segmented into 3 sections - and the middle section has an alternate waveform applied to it (to 2 of them, the other 2 ramps RF) - there are slits in the electrodes and ions are ejected out the top or/and bottom assuming there’s detectors there
issues: these slits make perturbations in the field need to be accounted for

138
Q

How does axial ejection in LIT work

A

Due to fringe fields - near edges, ions axial and radial motion can become linked - near the axial end for ejection can introduce repulsive DC forces (a cone) that prevents ions from getting over - excite via dipolar excitation to increase radial frequency which when coupled to axial increase axial energy to get over cone (efficiency 20%)

139
Q

tandem in space vs tandem in time

A

tandem in space is qqq tandem in time is trap

140
Q

types of qqq scans

A

, SRM/MRM (ion, ion), product ion(ion, scan), neutral loss (scan /scan), precursor scan(scan, ion)

141
Q

Why there might be pressure differences in a QQQ and benefits

A

so high pressure can be great for collisions (frags) also collisions cooling (if injecting a high energy ion cooling it can be good), ion molecule reactions etc, but lower pressure might be better for mass analysis (less broadening of ion packet - increase resolution etc)

142
Q

What does the type of collion gas matter

A

bigger - = less elastic collision - greater scattering (can also impart too much KE - cause fragmentation during scan - less resolution), smaller = more less frag less scatter

143
Q

What are the effects of space charge and when is it most prevalent

A

most prevalent at beginning of scan (low m/z ions) - can decrease resolution - cause mass shifts, and can shield from applied voltages (requires high cid voltage) -

144
Q

How does one counter space charge effects

A

autaomatic gain control

145
Q

Trap capacitance - whatis it and why does it matter

A

The ion trap is a capacitive load on the drive RF circuit (RLC and it’s tuned for that frequency - additional capacitance on top of that can throw it off -

146
Q

compare QIT and LIT

A

Simple cheap and easy MSN
OPERATING PRESSURE DIFFERENT
10-3 to 10-5 for LIT
QIT –RESOLUTION: is 10^3 -10^4
mass range 10^5 (commercially 2-8 k (2-4 on QIT)
QIT better analysis efficiency worse injection fficiency
Similar mass accuracy
Similar resolution
LIT better capacity

147
Q

QIT vs LIT - which can hold more ions,
better extraction efficiency , higher trapping efficiency. more amenable to hybrid instrumentation, is more prone to space charge

A

2d can hold more, 3d has better trapping efficiency, 2d has higher extraction efficiency, 2d more amenable to hybrid instrumentation and 3d more amenable to space charge

148
Q

Look at calculation for supplemental waveform

A
149
Q

For FTICR what are the major forces and equations used to derive them

A

Magnetic vs centrifugal; w = v/r (w is angular frequency) so w = zeB/m (note this is frequency in RADIANS per second)

150
Q

What is FTICR force dependent and independent of

A

independent of velocity dependent on unit charge, mag field, mass

151
Q

How are ions contained axially in an FTICR

A

containment lenses

152
Q

3 types of FTICR movement

A

Radial 9cyclotorn), radial (trapping) and MAGNETRON

153
Q

What causes the radius of the trapping motion and what is a consideration for it

A

The containment lenses and the initial K of the ion going into the trap. Equation is mv/Zeb = r (r is the radius of the cyclotron motion (so not the circling frequency but the larger radius of the motion is determined by our v)

154
Q

What causes the magnetron motion

A

trapped in z but pushed out by lorentz force - like it’s circling a hill

155
Q

Can the v and radius of cyclotron motion change?

A

Yes - it changes BUT W remains the same regardless of these changes (so they change in relation to each other (increase r , then v increases so same frequency

156
Q

Why is the trapping frequency not great for mass analysis

A

Very slow - poor resolution

157
Q

How does mangetron motion affect our cyclotron motion

A

The overall observed frequency is v cyclotron - v magnetron so it contributes to overall freequency

158
Q

magentron motion equation for FTICR

A

alpha (vt) / (Pi * a^2) * B) - alpha is constant based on shape, a is distance between plates and Vt is applied trapping voltage

159
Q

trapping frequency equation FTICR

A

vm = (1 / pi * a) (alpha * z * e * Vt / m )^ 1/2

160
Q

What are the effects of magnetron motion

A

Collisions collapse ion z-motion to the center of the trap
* Collisions reduce the cyclotron radius
* Collisions increase magnetron radius (radial diffusion), leads to ion loss from cell
* Alters the observed cyclotron frequency

161
Q

Describe excitation in an FTICR

A

initial cyclotron radius is small - apply a DIPOLAR RF excitation of same frequency - increase the v thus increasing the radius - this also bring them in to phase (or resonance ) with each other)

162
Q

Different types of FTICR excitation

A

Chirp vs SWIFT, CHIRP - is a quick sweep of the frequency range; Swift is you can choose the frequency - can eject/excite or note affect other ions

163
Q

CI reactions

A

write em (the main 3 steps is EI, then reagent gas reacts with more reagent gas and then we typically end with protonation of our M

164
Q

FTICR - w vs v

A

frequency in radians/s vs in HERTZ (v is in hertz) so v = w /2pi

165
Q

cyclotron radius, velocity and KE and important relations

A

this is mv/zeb; the velocity then is zebr/m and the KE is 1/2m(v^2) - so the cyclotron radius and velocity ARE dependant on kinetic energy velocity etc.

166
Q

What are the trapping frequency and magnetron frequency related to

A

Both proporitonal to alpha Vt, inverse proportion to a (magnetron a^2) where they differ is trapping frequency inverse proportion to m and magnetron inverse proportion to B

167
Q

How many charges do you need to detect current ICR

A

at leaast 100

168
Q

image charge equation

A

Q = -2zey/d (y is y idsplacement and d is diameter of cell(

169
Q

amplitude of current in ICR is related to what

A

independant of B and M - only related to # of ions

170
Q

FTICR data processing

A

So get an image current - thats in the time domain - fo a fourier transform to get into the frequency domain which can be converted to mass domain (through calibration)

171
Q

Resolution in ICR is based on what?

A

How long you can take image (better fits the waveform)more accurate sinusoidal wave)
R = vc*T/2 (limited by # of ions in cell and space charge)

172
Q

What is peak coalescnece and why important in ICR

A

If too many charges in cell - they will not be distinct packets but coalesce converge over time- limits charge and also amount of time you can listen for them

173
Q

Why do ion packets dephase naturally

A

given we’ve excited them - they’re going really fast - we have a low pressure to increase MFP BUt they gonna collide eventually (THIS IS WHY WE SEE SIGNAL DECAY)

174
Q

pressure of ICR

A

10^-9

175
Q

Notable FOM of FTICR

A

no scanning - 1 spectra instead of averaging over several (better for noise), no B or freq scanning means more stable, very high res and accurate mass
R = 10,000 to > 10 million
* Mass accuracy = <ppm
* Mass range: up to 10s of thousands
– Usually lower
– R gets worse at higher m/

176
Q

SORI CID explain

A

excite intermittently - r bigger so v bigger and then you pulse in a small amount of gas - since v higher - bam bigger hit more likely to frag

177
Q

What other parameters influence Rs in and ICR

A

B higher B - higher Rs , and Mz - smaller mz is higher Rs because large ion is SLOW so in our freuqneyc equation takes a long time to get one whole wave so takes a lot longer to get multiple waves and get a better image

178
Q

Magnetic field effect on mass range

A

higher better but doesnt linearly decrease plateaus - see chart

179
Q

ICR applications

A

whole protein analysis, isotope fine structure, sequencing etc, imaging

180
Q

notable FOM FTICR

A
  • R = 10,000 to > 10 million
  • Mass accuracy = <ppm
  • Mass range: up to 10s of thousands
    – Usually lower
    –non desturvice
  • Limited by ion/ion space charge interactions (100 to 105)
  • Efficiency can be low (long transients)
  • Slower than time of flight
  • Expensive
  • MSn
181
Q

Basis of electrostatic trap movement

A

ions circle around central electrode and their AXIAL (z) oscillation frequency is mass dependant
also vibration in radial direction

182
Q

Equation for orbitrap axial oscillation

A

w = ROOT( kz/m) k is field curvature - big takeaway is inversely related to root of m/z

183
Q

what is the axial oscillation frequency independant of

A

initial angle or velocity

184
Q

are the other forces besides axial oscillation frequency mass dependant? and if so can they mass analyze

A

They are but cannot mass analyze because they are radial motion and radially - our ions are all dispersed - not in packets - dephase really quickly (axially we do have packets) (also contributed to by space charge) (these forces relate to our axial oscillation frequency in addition to position in trap and size (distance between spindle and electrode)

185
Q

How does detection work in orbitrap

A

oscillate in z direction - have two electrodes on either end that pick up the image current -gets frequency signal - needs50-100 charges for detection

186
Q

under what conditions are ions injected into orbitrap

A

The spindle voltage is reduced - so that the electric field force matches and balances the KE of the ions (if too low - the ions neutralize on the spindle - if too high they hit the electrodes) - also done over short time span to maximize axial coherence - this lowering of the electric field causes ELECTRODYNAMIC SQUEEZING - an initial decrease of the radius (minimize ion loss increase efficiency)

187
Q

What is a C trap and what does it do

A

Ions stored external to orbitrap - elevactor method - raise potential here to get desired velocity - then dump - Drop RF - have orbitrap at ground - the ions head there - focus with DC (so even though c trap is curved and ions come from a curve- we focus to a point for injection)

188
Q

Resolution in orbitrap

A

similiar to FTICR - better for low m/z ions, relates to detection time - decreases with square root of m/z tho (FTICR is linearly);however FTICR can do longer analysis times

189
Q

Recent advances (how to make orbitrap better)

A

stronger electric field - means (decrease our inner and outer electrode radii -resulting in stronger field strength which means stronger frequencies increases resolutoin

190
Q

Orbitrap FOM

A

Cheaper than ICR (no big cryomagnet)
* High resolution (not as high on the top end as ICR, but still very
good), ~100k-400k
* Store more ions before space charge limit than ICR
* High mass accuracy (1-5 ppm), DC fields can be made very stable
* m/z range: normally up to 6000
* Dynamic range = 103

191
Q

How does an electrostatic linear ion trap work

A

two reflectrons essentially - ion is bounced back and forth - to get ions in - ramp one reflection down - to get them out do the same

192
Q

Benefits of electrostatic linear trap

A

largely field free so no issues from field imperfections (or less), can be compact and cheap, and can do ms/ms with just the one analzyer

193
Q

very basically what is charge detection ms

A

simultaneous measurement of m and z so can directly just get mass

194
Q

How can hybrid instrumentation increase signal (CASI)

A

ion accumulation! can filter one mass and accumulate in a hexapole - this is great because if looking at mass range - additional limitations, space charge etc - relatively not as strong etc

195
Q

rule of data dimesnionailty

A

its multicplicative (if can seperate 100 componnds here 100 on this orthogonal seperaiton - can separate 10000 total

196
Q

what is parallel analyses

A

basically one mass analyzer doing somethgin whiel another more self sufficient one is running different scan s eg LIT and orbitrap - the LIT can do all on its own - fragment, analyze etc while orbitrap running

197
Q

go through som ehybrid instrument diagrams and label them

A
198
Q

3 major MS detectors

A

faraday cup, ion image and EM

199
Q

How does a faraday cup work

A

ion hits - neutralizes - in neutralization electrons move in cup to cause neutralization - this causes a current

200
Q

Faraday cup FOM

A

cheap, precise, NOT velocity dependant - good- however low sensitivity, and low response time, is destructive

201
Q

How do EM detectors work and name some types

A

a neutral Or an ion hits a dynode - and releases some electrons (the amount is a result of the work function of the material - and generally this will cause electrons to hit another dynode and cause a cascade - amplifying our signal (10^6-10^8

202
Q

EM FOM

A

amplification, destructive, fast, however short life time , dependant on impact velocity and KE (less precise - mass bias) VERY sensitive! eg yoctomolar sensitivity in TOF

203
Q

Image current = describe

A

non destructive

204
Q

2 types of noise

A

chemical (variation in sample, chemistry of system, temp, pressure , rxn etc), instrument (each electrical component has own noise - eg thermal, shot, flicker, environment)

205
Q

What is thermal johnson noise and how do we improve

A

thermal agitation of electrons in circuit (only stopped at absolute 0- dependant on Temp, resistance elements and frequency bandwidth (all proportional to) - so we can decrease any of those (use less resistive elements, cool it or decrease frequency bandwidth(that does make instrument slower though)

206
Q

What is shot noise and how do we improve

A

Poisson noise - the idea that all of the movements of electrons to make our electricity is just an average of a lot of discrete moves - more variance than really being seen and that can be noie - related to eI and frequency)

207
Q

Environmental Noise what is it

A

instrument surrounding - pickup induction of frequencies around us eg radio or power

208
Q

What are ttwo ways to improve signal to noise

A

Hardware(grounding, shielding, difference amplifiers, filters) vs software (signal averaging(boxcar go 3 at a time), digital filtering and smoothing),

209
Q

How does averaging increase signal to noise

A

proprtional to root of N (# of average syou take

210
Q

Why is vacuum required in MS

A

Preseven tcollisions - because these cause SCATTERING and unwanted REACTIONS and FRAG

211
Q

What type of excitation is EI

A

EI is always vertical since our electrons are moving way faster than the freuqneyc of the bond - adiabatic means no frag

212
Q

If we ahve good franck condon factors - what does it mean about the eleectorn ejected

A

probably non bonding

213
Q

CI vs APCI force driving reaction

A

kinetci vs thermodynamic - CI is based on concentration and APCI is based on Proton affinity

214
Q

how to get mean free path

A

1 / (root(2) CCS * N

215
Q

How to do selected ion injection

A

So the equation is 4eVN / (m *r^2 * frequency^2) each is e - is 1.6e-19, V is given (instrument specific), N is avogadros, m is mass but needs to be in kg/mol (so if molar mass /1000), r^2 needs to be in meter^2; frequency needs to be in radians (if in megahertz *6.28 *100000) and if calculated out it gives us Q We can then use Q to solve for Beta ( Beta - ROOT(a + q^2/2). And then we can use beta to solve for our secular frequency - W = (n + 1/2 * Beta) * Frequency (n is a constant often -/5 1 or 0)

216
Q

convert daltons to kg

A

x1.66E-27

217
Q

How to get collision rate

A

N* kcoll

218
Q

How to get N

A

3E16 * pressure

219
Q

Ambient pressure in pascal

A

101325 (if doing it for API however off by 100? idk how

220
Q

Aperture equation

A

Xm/D = 0.67 root (po/p)

221
Q

Why is nesi better than esi

A

Can spray pure H2o
-lower sample usage
-higher sensitivity
-more tolerant to nonvolatile salts
-Lessfission events due to starting with smaller droplets – means lower salt concentration in first droplet
Greater surface area to volume ratio in NESI

222
Q

what to avoid in ESI

A

non volatile salts and solvents that have really high surface tensions

223
Q

range acuracy and r for ll analyzers

A

FO

R

TOF - 60-70k
Sector - 10-100k
Quad - 2-8k
FTICR -p tp 10 illion
3dand LIT - 1000-10000
Oritrap 100-400k

RANGE
TOF - theoreticaly unliit
Sector - up to 10k
Quad 1-2k
3d andLIT -10^5but coercially 2-4or8k)
FTICR - 10k to 10’s of thousands
orbitrap - up to 6k

SENSITIVITY
TOF - single digit pp
FTICR - sub pp
Sector - pp
QQQ - 10’s of pp
3d trap - 50’s-100 of pp’s
Orbitrap - single digit

224
Q

What is velocity in FTICR equation

A

zeB*r over m

225
Q

After exitation in FTICR once the dipolar RF up is over - what happens to the excited ion radius (of cyclotron otion)

A

stays big

226
Q

Rsolution equation in ters of tie and v in fticr

A

R = v*t div 2

227
Q

What is peak colaescnecnedepenant on

A

Magnetic field strength
– The ion frequencies
– The number of charges
– The excitation voltages

228
Q

What is felgetts advantage

A

FTICR does one scan = good for signal to noise ecause not averaging the noise fro several spectra - just one st

Chem Bio (17 decks)

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