Mass Analyzers Ion movement

Mass Analyzers
Árpád Somogyi
CCIC MSP
OSU Summer Workshop
Ion movement
• Biased metal plates (electrodes, lenses) used to
move ions between ion source and analyzers
• Electrodes and physical slits used to shape and
restrict ion beam
• Good sensitivity is dependent on good ion
transmittance efficiency in this area
Mass
analyzer
Ionization
source
inlet
all ions
Detector
sorted
ions
Data
system
1
Ion detection
• Ions can be detected efficiently w/ high
amplification by accelerating them into surfaces
that eject electrons
Mass
analyzer
Ionization
source
inlet
all ions
Detector
sorted
ions
Data
system
Detectors
TOF
2
Ion energy
• Kinetic energy of ions defined by
E = zeV = qV = ½ mv2
E = kinetic energy
m = mass
v = velocity
e = electronic charge (1.60217e-19 C)
z = nominal charge
V = accelerating voltage
Learning Check
Consider two electrodes,
one at 1000 V and one at ground (0 V)

1000 V
0V
+ ion will travel with kinetic energy of ___________
3
Question:
Consider an ion source block and an
extraction lens. How would you bias the block and
lens if you want the ions to be accelerated by
a) 8000 eV (appropriate for magnetic sector)
b) 5 eV (appropriate for entering a quadrupole)
c) 20,000 eV (appropriate for entering a TOF)
Notice: accelerating voltages vary with analyzer
(has consequences for MS/MS)
• High voltage (keV energy range)
– magnet (B)
– electrostatic (E)
– time-of-flight (TOF)
• Low voltage (eV energy range)
– quadrupole (Q)
– ion trap (IT, LT, OT)
– ion cyclotron resonance (ICR)
4
Mass Resolution
• Mass spectrometers separate ions with a
defined resolution/resolving power
• Resolving power- the ability of a mass
spectrometer to separate ions with
different mass to charge (m/z) ratios.
Example of ultrahigh resolution
in an FTICR
J. Throck Watson “Introduction to Mass Spectrometry” p. 103
5
Resolution defined at 10% valley
M
R=M/∆M
∆M
General about mass
spectrometers
• Common features
– Accelerated charged species (ions) interact
with/can be controlled by
• Electrostatic field (ESA, OT)
• Magnetic field (B, ICR)
• Electromagnetic (rf) fields (Q, IT, LT)
– Or ions just fly (TOF)
6
For each of the following applications, choose the most
appropriate mass analyzer from the following list.
orbitrap (OT)
time-of-flight (TOF)
quadrupole (Q)
FTICR
Analyzer
Purpose
______
synthetic organic chemist wants exact mass of
compound
biochemist wants protein molecular weight of
relatively large protein (MW 300,000)
EPA (Environmental Protection Agency) wants
confirmation of benzene in extracts from 3000
soil samples
Petroleum chemist wants to confirm the
presence of 55 unique compounds at one
nominal mass/charge value in a mass spectrum
_______
_______
_______
Desirable mass spectrometer
characteristics
7
Desirable mass spectrometer
characteristics
1)
They should sort ions by m/z
2)
They should have good transmission (improves
sensitivity)
3)
They should have appropriate resolution (helps
selectivity)
4)
They should have appropriate upper m/z limit
5)
They should be compatible with source output
(pulsed or continuous)
Mass spectrometers record m/z
values
m/z values are determined by actually measuring different
physical parameters
Type of analyzer
•
•
•
•
•
electric sector
magnetic sector
quadrupole, ion trap
time-of-flight
FT-ion cyclotron resonance
Physical parameter used as
basis for separation
•
•
•
•
•
kinetic energy/z
momentum/z
m/z
flight time
m/z (resonance frequencies)
8
Types of Mass Analyzers
• Magnetic (B) and/or Electrostatic (E) (HISTORIC/OLDEST)
• Time-of-flight (TOF)
• Quadrupole (Q)
• Quadrupole Ion Trap (IT)
• Linear Ion Trap (LT)
• Orbitrap
• Fourier Transform-Ion Cyclotron Resonance (ICR)
Performance Advantages / Disadvantages / $$$
TOF
Quadrupole
Quadrupole Ion trap
FTICR
Orbitrap
9
MS and MS/MS
Ionization Analysis
MS:
Collide with
target to produce
fragments
MS/MS:
Ionization
Selection Activation
Analysis
http://www.iupac.org/goldbook/T06250.pdf
10
Tandem in Space
Triple quadrupole
Collisions with gas μsec dissociation
Tandem in Time MS/MS
T1
T2
T3
Collisions with gas msec dissociation
11
Current popular MS/MS
arrangements (2012)
Tandem in Space
QqQ
Q Trap
Q TOF
TOF TOF
LTQ-Orbi (& QExactive)
Tandem in Time
Ion Trap (2 or 3 D)
FT-ICR (FT)
Decision factors when choosing a
mass spectrometer
• Speeeeeeeeeeeeed
•R e s o l u t i o n
•
Sensitivity
•D na ic ang
y
m
r
e
• Co$t
12
Quadrupole
TOF
Quadrupole Ion trap
FTICR
Orbitrap
Time of Flight
m/z
V
KE = zeV = ½mv2
v = D/t
½m(D/t)2 = zeV


t= m 
 2zeV 
1/ 2
Detector
D
m = mass
V = velocity
D = distance of flight
t = time of flight
KE = kinetic energy
e = charge
D
13
How does the ion generation
step in TOF influence m/z
analysis?
Consider MALDI
h
Target
Matrix
+
Analyte
Analyte ion may have (1) Kinetic Energy
distribution or (2) Spatial distribution
How will KE spread influence
the spectrum?
Ions of same
m/z
Has
slightly
greater KE
Effect is broad
peaks
c/o Cotter
14
How will KE spread influence
the spectrum?
Solution to peak broadening caused by
kinetic energy spread:
Reflectron (ion mirror)
Series of ring electrodes, typically
with linear voltage gradient
Time-of-Flight Reflectron
• Increased resolution by compensating for KE spread from the
source
http://www.jic.bbsrc.ac.uk/services/proteomics/tof.htm
15
Reflectron TOF
Reflectron
Mass Analyzer
(TOF)
Detector
Ion Source
(MALDI)
x
x
x
x
x
High resolution
KE = ½ mv2
Reflectron TOF
Mass Analyzer
(TOF)
Reflectron
Detector
Ion Source
(MALDI)
x
High resolution
KE = ½ mv2
16
http://www.abrf.org/ABRFNews/1997/June1997/jun97lennon.html
We talked about how
to deal with kinetic
energy spread.
How do we deal with
ions formed at
different locations in
the source (spatial
distribution)?
17
Delayed Extraction
10 KV
10 KV
+ +
+
+
+
+
+
+
+
+
7 KV
Low mass (below 40 k Da)
High resolution
Continuous vs. Delayed Extraction
Continuous TOF
Resolution = 700 (FWHM)
Delayed Extraction
Resolution = 6000 (FWHM)
18
In te n s. [a .u .]
Recent TOF designs: improved resolution, better sensitivity and mass accuracy
(Ultraflex III MALDI TOF-TOF)
* Pepmix\0_N6\1\1SRef
3145.708
6000
Resolution: 25,000
S/N: 46
5000
4000
3000
2000
3177.722
1000
0
3140
3145
3150
3155
3160
3165
3170
3175
3180
3185
m/z
Typical TOF Specs
• m/z Range: unlimited u
• Resolution: ~20,000
(Reflectron)
• Mass Accuracy: ~ 3-10
ppm (300-4,000 u)
• Scan Speed: 106 u/s
• Vacuum: 10-7 Torr
• Quantification: low medium
• Positive and
Negative Ions
• Variations:
Linear, Reflectron,
• Tandem: w/ quads,
TOFs and/or sectors
19
TOF
Quad
3D Trap
Linear Trap
FT‐ICR
Orbitrap
mass range
Resolution
exact m/z
sensitivity
all ion detection
ion storage
speed
dynamic range
quantification
MS/MS types
sample introduction
simplicity
cost/performance
Can an MS/MS instrument be
constructed if the only analyzer
type available is TOF?
20
TOF-TOF
http://docs.appliedbiosystems.com/pebiodocs/00106293.pdf
High-energy (keV) Collisions
with Gas in a TOF-TOF
21
16O/18O-labeled
DLEEGIQTLMGR
*Resolution
Medzihradszky, KF et al. Anal Chem. 2000, 72: 552-558
Intens. [a.u.]
High (keV) collisions allow for w peptide ions and immonium ions
x104
328.574
6
492.623
981.346
5
4
656.765
186.600
146.669
3
821.038
2
120.694
1
284.552
90.771
443.572
612.695
721.026 776.938
941.468
0
200
400
600
800
1000
m/z
MALDI TOF-TOF fragmentation spectrum of a sodiated polymer
O
O
O
CH2 CH2 *
m
n
3-OEB, m=1-3 (164, 44)
Copolymer of 2-hydroxybenzoic acid and ethylene carbonate
22
Advantages and Disadvantages
Mass Spectrometer
Advantages
Disadvantages
TOF-TOF
high resolution, high
m/z fragment ions
Large size
keV CID
Not ideal for
continuous
ionization source
easier de novo
peptide sequencing
$$$
dn and wn to
distinguish Ile/Leu
MALDI source
Analyzers
TOF
Quadrupole
Quadrupole Ion trap
FTICR
Orbitrap
23
Quadrupole (Q)
http://www.files.chem.vt.edu/chem-ed/ms/quadrupo.html
Quadrupole (Q)
• four parallel rods or poles
• fixed DC and alternating RF voltages
rf voltage
+dc voltage
rf voltage 180° out of phase
-dc voltage
• only particular m/z will be focused on the
detector, all the other ions will be deflected into
the rods
• scan by varying the amplitude of the voltages
– (AC/DC constant).
24
Quadrupole Field Animation
Positive rod
Negative rod
Positive rod
Negative rod
http://www.kettering.edu/~drussell/Demos/MembraneCircle/Circle.html
negative DC offset
-DC
+
-
positive DC offset
+
+DC
25
Ion Motion in Quadrupoles
- a qualitative understanding
• + DC, ions focused to center
• - DC, ions defocused
• +DC w/ rf, light ions respond to rf, eliminated
(high mass filter)
• -DC w/ rf, light ions respond to rf, focused to
center (low mass filter)
26
Quadrupole animation
http://www.youtube.com/watch?v=8AQaFdI1Yow&feature=related
http://www.youtube.com/watch?v=pjCun7QF19U
Initial kinetic energy affects ion motion in quad
27
Figure 9. The a-q stability diagram: a) The shaded area represents those areas in a-q space
which correspond to stable solutions of Mathieu’s differential equation. B) The one amu
bandpass mass filter: Notice that only ions of m/e m+1 fall within the stability diagram.
Miller, P., Denton, M.B., J.Chem Ed., 63:7, pg 617, 1986.
Quadrupole Typical Specs
• m/z Range: 2-4000 u
• Resolution: Unit
• Mass Accuracy: ca +/0.1 u
• Scan Speed: 4000 u/s
• Vacuum: 10-4 – 10-5
Torr
• Low Voltages:
RF ~6000 –10000 V
DC ~500V-840V
Source near ground
• Quantification: good
choice
• Positive and Negative
Ions
• Variations: SingleQ,
TripleQ, Hybrids
28
TOF
Quad
3D Trap
Linear Trap
FT‐ICR
Orbitrap
mass range
Resolution
exact m/z
sensitivity
all ion detection
ion storage
speed
dynamic range
quantification
MS/MS types
sample introduction
simplicity
cost/performance
What MS/MS instruments can be
produced from Q?
What MS/MS instruments can be
produced from Q and TOF?
29
Triple Quadrupole
- since 1970’s and still going strong!
Q1
Q3
Q2
S
D
Attractive Features:
• Source near ground and operates at relatively high pressure
Couples well to source and to chromatography
•Multiple scan modes easy to implement
Triple Quadrupole (QQQ)
Detection
System
Dynode
Turbo
Q3
Source
Q0
Q3
Q1
Q2
Heated
Capillary
Q2
Q1
Q0
Q00
c/o Thermo Finnigan Corp.
c/o Agilent Corp.
30
MS/MS Scan Modes
Product Ion Scan
Select
Dissociate
Scan
Scan
Dissociate
Select
Scan
Dissociate
Scan
Select
Dissociate
Select
Precursor Ion Scan
Neutral Loss Scan

Selected Reaction
Monitoring (SRM)
Scan
300
Voltage
Analyte
Mixture
100
200
RF
DC
100
200
300
Vm1
m/zm1
Vm2
m/zm2
Vm3
m/zm3
mass spectrum
31
Scan
300
Voltage
100
Analyte
Mixture
200
RF
DC
100
200
300
Vm1
Vm2
Vm3
100
300100
100
300
200200 300
100
200 300
200
Scan
300
Voltage
Analyte
Mixture
100
200
RF
DC
100
200
300
Vm1
Vm2
Vm3
100
300100
100
300
200200 300
100
200 300
200
32
Scan
RF
300
Voltage
100
Analyte
Mixture
200
DC
100
200
300
Vm1
Vm2
Vm3
100
300100
100
300
200200 300
100
200 300
200
Select
Voltage
200
Analyte
Mixture
RF
DC
100
200
300
Vm2
Desired
Analyte
m/zm2
mass spectrum
33
Modes of scanning in a Triple Quadrupole (QQQ)
Q1
scan or
select
q2 (gas)
rf only
Q3
scan or
select
• Quadrupole is a mass filter
• QQQ used in this tutorial to describe scan modes
– Q1 and Q3 = analyzers
– q2 (middle quadrupole) used for CID (dissociation)
• Ways to set quadrupoles: Scan, Select & rf only
• Other instruments are used: Q-tof, Q-trap, Linear TrapOrbitrap, Trapping instruments
Quadrupole Time of Flight
(Q-TOF)
http://www.waters.com/WatersDivision/waters_website/products/micromass/ms_top.asp (outdated)
34
Low-energy (eV) Collisions
with Gas
Q-TOF
80 fmol BSA digest
QQQ
Shevchenko, A., et al., Rapid. Commum. Mass Spectrom., 1997, 11: 1015-1024
35
QTOF with Ion Mobility
Analyzers
TOF
Quadrupole
Quadrupole Ion trap
FTICR
Orbitrap
36
What is small, inexpensive
and still gives great MSMS ?????
Quadrupole Ion Traps
Miniature IT: Cooks, R. G. and coworkers
Anal. Chem. 2002, 74, 6145-6153; 2000, 72, 3291-3297.
http://www.chem.wm.edu/dept/faculty/jcpout/faculty.html
Ion path in a trap
37
Quadrupole Ion Trap (QIT)
http://www-methods.ch.cam.ac.uk/meth/ms/theory/iontrap.html
Quadrupole Ion Trap (QIT)
• Quadrupole ion trap mass analyzer consists of three
hyperbolic electrodes: the ring electrode, the
entrance end cap electrode and the exit endcap
electrode.
• Ions enter trap through inlet focusing system and
entrance endcap electrode.
• An AC potential of constant frequency and variable
amplitude is applied to the ring electrode to produce
a 3D quadrupolar potential field within the trapping
cavity which traps ions in a stable oscillating
trajectory confined within the trapping cell.
• The oscillating trajectory is dependent on the trapping
potential and the mass-to-charge ratio of the ions.
• During ion detection, the electrode system potentials
are altered to produce instabilities in the ion
trajectories and thus eject the ions.
38
Quadrupole Ion Trap (QIT)
3D - Quadrupole Ion Trap (Demo)
39
Activation:
Low-energy (eV) Collisions
with Gas
IRMPD
(Infrared Multiphoton Dissoc)
Research: Micro CIT Array
Matt Blain, Sandia
Cooks, Purdue
1.8 µm
2.4 µm
Top End Cap Array
Ring Electrode Array
Bottom End Cap Array
Collector Array
40
QIT Typical Specs
• m/z Range: 20-6000 u
• Resolution: Unit
• Mass Accuracy: ca +/0.1 u
• Scan Speed: 4000 u/s
• Vacuum: 10-3 Torr
• Quantification:
possible, not accurate
• Positive and
Negative Ions
Advantages and Disadvantages
Mass Spectrometer
Advantages
Disadvantages
QIT
Compact
Limited storage of
ions limits the
dynamic range of the
ion trap (space
charge effect)
MSn
1/3 of low mass
range lost in MS/MS
mode, typical
operation
Data dependent
scanning
Relatively
inexpensive
Low E collisions
41
Advantages and Disadvantages
Mass Spectrometer
Advantages
QIT
Disadvantages
Poor quantification
Sensitive
Collision energy not
well-defined in CID
MS/MS
Mass Accuracy
To increase mass accuracy in a
Trap  LT, orbitrap, FT-ICR
RF ION TRAP ELECTRODE
STRUCTURES
LCQ-Type 3D
Quadrupole Trap
LTQ-Type (2D)
Linear Quadrupole Trap
ASMS Fall Workshop
2006 JEPS
42
2D vs. 3D Ion Traps
Ion Transfer
Tube
Skimmer
Tube Lens
Linear Trap Demo
Ion Transfer
Tube
Skimmer
Tube Lens
43
Estimating Relative Ion Storage Capacity
3D Ion vs Linear (2D) Quadrupole Ion Traps
3D RF Quadrupole
Ion Trap
2D RF Quadrupole
Linear Ion Trap
z
z
y
L
y
x
x
R3D
~ Spherical Ion Cloud
R2D
~ Cylindrical Ion Cloud
ASMS Fall Workshop
2006 JEPS
Overall Performance Gains
LTQ
3D Traps
Increase
•Trapping efficiency
~ 55-70%
~5%
~ 11-14x
•Detection efficiency
~ 50-100%
~50%
~ 1-2x
•Trapping capacity
~ 20,000 ions
~500 ions
~ 40x
44
Motivating Factors Realized
• Increased Trapping Efficiency
• Increased Trapping Capacity
Which means....
• Increased Sensitivity
• Increased Inherent Dynamic Range
• Increased S/N for full Scan MS
• Practical MSn
•Faster Scan Times - no μscans (only one)
How are 3-D traps and linear
ion traps used in MS/MS
Stand alone
3-D traps
LTQ
Front or back end of tandem-in-space
LT-TOF
LT-FT, LT-Orbitrap,
QTrap
45
LIT and QTrap; Different ways of using Linear Traps
~ 100% of ions trapped are
detected due to radial ejection
Linear Ion Trap
Skimmer
Axial ejection allows for hybridization
– without compromise (FT)!
Majority of trapped ions
cannot be scanned out
Hybrid Quadrupole Trap
~ 15% detected*
Axial ejection depends on fringe fields generated by grid –
this grid compromises triple quadrupole performance
*Hager, J., RCM., 2003, 17, 1389
9 Protein Mixture
9 Protein Mixture Peptide Identification
73
80
70
61
Number of Peptides
60
50
42
35
40
30
20
31
21
Deca XP plus
LTQ
24
12
10
0
10min
20min
30min
Gradient (min)
60min
46
Activation:
CID
Low-energy (eV) Collisions
with Gas
IRMPD
(Infrared Multiphoton Dissoc)
ETD
(electron transfer dissociation)
TOF
Quad
3D Trap
Linear Trap
FT‐ICR
Orbitrap
mass range
Resolution
exact m/z
sensitivity
all ion detection
ion storage
speed
dynamic range
quantification
MS/MS types
sample introduction
simplicity
cost/performance
47
Analyzers
TOF
Quadrupole
Quadrupole Ion trap
FTICR
Orbitrap
For a charge q moving with a velocity of v in a magnetic field B
there exists a force (F) which is perpendicular to the plane determined
by v and B.
48
Analyzers based on magnetic fields: ICR
Magnetic forces move ions in a circular path
demo
http://www.casetechnology.com/implanter/magnet.html
Cyclotron motion of an ion in a magnetic field (B).
Note: ion motion is much more complex due to the presence of
electrostatic field (magnetron/cyclotron motion, see below)
49
50
a
b
c
C9H16N5
194.1405
time (ms)
C11H20N3
C7H12N7
194.1154
194.1657
Modified van Krevelen diagram for LDI ions
51
11+
12+
10+
9+
Charge state/MW determination
for proteins
∆m
= z
∆(m/z)
Carbons
isotopes so
∆m=1 Da
Calc ∆(m/z)
52
FTICR animation
http://www.youtube.com/watch?v=a5aLlm9q-Xc&NR=1
New ICR cell design
by E. Nikolaev et al.
E. Nikolaev et al., Initial Characterization of a New Ultrahigh Resolution
FTICR Cell with Dynamic Harmonization, JASMS, 2011, 22, 1125-1133.
E. Nikolaev and coworkers, Twelve Million Resolving Power on 4.7T FT-ICR
Instrument with Dynamically Harmonized Cell – Observation of Fine Structure
In Peptide Mass Spectra, JASMS, 2014, 25, 790-799.
53
Bruker 9.4 T FT-ICR Apex-Qh Tandem Mass Spectrometer
MALDI
Dual source, MS only, no ion selection
ESI
QCID (eV) MS/MS
Ion selection and activation in the ICR
IRMPD, SORI, ECD
HDX in the ICR cell
54
Activation:
SORI CID
Low-energy (eV) Collisions
with Gas (off resonance)
RE
(resonance excitation)
IRMPD
(Infrared Multiphoton Dissoc)
ECD
(electron transfer dissociation)
Intens.
x107
3.0
MS/MS spectra depend
on
i) Charge state
ii) Ion activation method
iii) Collision energy
2.5
YIGSR_QCID_22eV_000002.d: +MS2(595.0)
MH+
QCID 22 eV
249.1593
595.3171
2.0
1.5
302.1453
1.0
175.1186
560.2803
0.5
408.1864
90.2256
0.0
x108
(more details in the
Ion Activation
Methods
by Vicki Wysocki)
1.5
YIGSR_doubly_QCID_6eV_000001.d: +MS2(298.0)
[M+2H]2+
QCID 6 eV
319.1718
1.0
249.1593
y5
0.5
277.1541
432.2552
136.0756
0.0
x107
2.0
465.2077
YIGSR_doubly_IRMPD_40P_0_30s_000001.d: +MS2(298.0)
[M+2H]2+
IRMPD 30s, 30%
298.2804
1.5
1.0
249.1644
0.5
102.7325
595.3466
0.0
100
200
300
400
500
600
m/z
55
FTICR Typical Specs
• m/z Range: > 15000 u
• Resolution: High, 106
• Mass Accuracy: 100
ppb
• Scan Speed: slow
• Vacuum: 10-9- 10-11Torr
• Quantification:
possible, not accurate
• Positive and
Negative Ions
Advantages and Disadvantages
Mass Spectrometer
Advantages
Disadvantages
FTICR
Highest recorded
mass resolution of all
mass spectrometers
Limited Dynamic
Range
MSn
Low E collisions
Non-destructive ion
detection
High vacuum
Low presure
(difficult GC/LC
coupling)
Accurate mass
measurement
Big size
Powerful capabilities
Not a high
for ion chemistry
throughput technique
experiments (ionmolecule rxns)
56
TOF
Quad
3D Trap
Linear Trap
FT‐ICR
Orbitrap
mass range
Resolution
exact m/z
sensitivity
all ion detection
ion storage
speed
dynamic range
quantification
MS/MS types
sample introduction
simplicity
cost/performance
Analyzers
TOF
Quadrupole
Quadrupole Ion trap
FTICR
Orbitrap
57
Orbitrap Readings
Pictured: August 2009 cover of J. Am. Soc. Mass Spectrom.
A New Kind of FTMS: The Orbitrap
58
How does it trap ions?
• Quadro-electrostatic field (Orbital trapping of ions)
– Electrostatic field with potential distribution
• Field is the sum of the quadrupole field of the ion trap and the logarithmic
field of the cylindrical capacitor (center electrode)
U(r/z) = k/2(z2 – r2/2) + k/2(Rm)2ln[r/Rm] + C
– Electrodynamic squeezing
• Ions entering with a tangential velocity (acceleration voltage) are pulled
into orbit around center electrode due to a voltage drop on the center
electrode
Orbitrap
59
LTQ Orbitrap™ Hybrid MS
Finnigan LTQ™ Linear Ion Trap
API Ion source
Linear Ion Trap
Differential pumping
C-Trap
Orbitrap
Differential pumping
LTQ Orbitrap Hybrid MS
System Integration
Finnigan LTQ™ Linear Ion Trap
Gas <1 mtorr
V
x
-2 k V
Central
Electrode
Voltage
-3.5 k V
60
Lord of the ion rings: Retainment of the rings
Image current detection on
split outer electrodes
k
m/ z

1. Frequencies are determined using a Fourier Transformation
2. For higher sensitivity AND resolution, transients should not decay too fast
Ultra-high vacuum
Ultra-high precision
http://apps.thermoscientific.com/media/SID/LSMS/Video/webinar/orbitrap_elite/animation/
http://www.youtube.com/watch?v=KjUQYuy3msA
Ion Motion in the Orbitrap
Simulation of ion trajectory with SIMION
Characteristic frequencies
– Frequency of rotation ωφ
 
z
2
 Rm 

 1
2  R 
2
 Rm 
 2
 R 
– Frequency of radial oscillations ωr
r   z 
– Frequency of axial oscillations ωz
z 
k
m/q
61
Orbitrap --Resolving Power
+5
Insulin: m/z = 5733
Charge state: +5, +4 and +3
+3
+5
m/m = 70,000
+4
1,200
1,400
1,600
1,800
2,000
m/z
+4
1,147
1,148
m/z
1,149
m/m = 45,000
+3
m/m = 40,000
1,434
1,435
1,436
m/z
R. Noll, H. Li, 2002
1,911
1,912
m/z
1,913
1,914
Orbitrap LTQ Velos: Analysis time
High resolution acquisition
R = 7,500
R = 15,000
R = 30,000
R = 60,000
R = 100,000
R = Time
Low resolution acquisition
R = unit
Figure adapted from
Olsen J V et al. Mol Cell Proteomics 2009;8:2759-2769
62
http://fscimage.thermoscientific.com/images/D13092~.pdf
63
translation inhibitor endoribonuclease
[Clostridium difficile BI1]
High Resolution Fragments
Charge: +3, Monoisotopic m/z: 744.71710 Da (-1.83 ppm),
MH+: 2232.13675 Da, RT: 67.42 min,
High Resolution Fragments
Fragment Errors (ppm, partial list)
64
Manual
http://sjsupport.thermofinnigan.com/techpubs/manuals/LTQ-OrbitrapVelos_Start_2_6_0.pdf
Video
http://www.youtube.com/watch?v=-u1keatKtMI
Application/Optimization
TOF
Quad
3D Trap
Linear Trap
FT‐ICR
Orbitrap
mass range
Resolution
exact m/z
sensitivity
all ion detection
ion storage
speed
dynamic range
quantification
MS/MS types
sample introduction
simplicity
cost/performance
65
Instrument Performance for Proteomic Applications
Han et al., Curr. Opin. Chem. Biol. 2008; 12(5):483-490.
Learning Check
Draw the appearance of the mass spectrum in which
both singly and doubly charged YGGFLR (molecular
weight 711.3782) are produced and analyzed with a
quadrupole, TOF and orbitrap (Hint: peaks widths
important)
66
712 in Quad, TOF, ICR
Intensity
QUAD
Intensity
TOF
m/z
m/z
Intensity
ICR
m/z
General Conclusions
•
•
•
•
•
Many instruments are complementary
More Activation methods, the better
Assess your needs
Assess your budget
@ Research level, may want to build
your own
67
Suggested Reading List
GENERAL MS AND MS/MS
Kinter, M. and Sherman, N. E., Protein Sequencing and Identification Using Tandem Mass Spectrometry,
Wiley and Sons, New York, NY, 2000.
De Hoffmann E., Mass Spectrometry – Principles and Applications (Second Edition), Wiley and Sons,
New York, NY, 2002.
Busch, K.L., et al., Mass spectrometry/ mass spectrometry: techniques and applications of tandem
mass spectrometry, VCH Publishing, New York, NY, 1988.
McLafferty, F.W. (Ed) Tandem Mass Spectrometry, Wiley and Sons, New York, NY, 1983.
McLafferty, F.W. and Turecek, F. Interpretation of Mass Spectra, University Science Books, New York, NY, 1993.
Siuzdak, G. Mass Spectrometry for Biotechnology, Academic Press, San Diego, CA, 1996.
Gygi, S.P. and Aebersold, R., Curr. Opin. Chem. Biol., 4 (5): 489, 2000.
Roepstorff, P., Curr. Opin. Biotech., 8: 6, 1997.
De Hoffmann, JMS, 31: 129, 1996.
Mann, M. et al., Annu. Rev. Biochem., 70: 437, 2001.
McLuckey, S and Wells, J.M., Chem. Rev., 101: 571, 2001.
Suggested Reading List
Q-TOF
Morris, H.R. et al., J. Protein Chem., 16: 469, 1997.
Shevchencko A., et al., Rapid Commun. Mass Spectrom., 11: 1015, 1997.
Shevchencko A., et al., Anal. Chem., 72: 2132, 2000.
Medzihradszky, K.F., et al., Anal. Chem., 72: 552, 2000.
Glish, G.L. and Goeringer, D.E., Anal. Chem., 56: 2291, 1984
Morris, H.R. et al., Rapid Commun. Mass Spectrom., 10: 889, 1996.
Wattenberg, A. et al., JASMS, 13 (7): 772, 2002.
Lododa, A.V. et al., Rapid Commun. Mass Spectrom., 14(12): 1047, 2000.
TOF
Bush, K., Spectroscopy, 12: 22, 1997.
Cotter, R.J., Time-of-Flight: Instrumentation and Applications in Biological Research, ACS, Washington, DC, 1994.
68
Suggested Reading List
TOF-TOF
Yergey, A.L. et al., JASMS, 13 (7): 784, 2002.
Go, E.P. et al., Anal. Chem., 75: 2504, 2003.
FTICR
Buchanan, M.V. (Ed), Fourier Transform MS, ACS, Washington, DC, 1987.
Comisarow, M.B. and Marshall, A. G., Chem. Phys. Lett., 25: 282, 1974.
McIver, R.T. et al., Int. J. Mass Spectrom. Ion Processes, 64: 67, 1985.
Kofel, P. et al., Int. J. Mass Spectrom. Ion Processes, 65: 97, 1985.
Williams, E. R. Anal. Chem., 70: 179A, 1998.
McLafferty, F. W. Acc. Chem. Res., 27: 379, 1994.
Fridriksson, E. K. et al., Biochemistry, 39: 3369, 2000.
Fridriksson, E. K. et al., Biochemistry, 38: 8056, 1999.
Kelleher, N. L.et al., Protein Science, 7: 1796, 1998.
McLafferty, F. W. et al., Int. J. Mass Spectrom., 165: 457, 1997.
.
Suggested Reading List
Green, M. K. and Lebrilla, C. B. Mass Spectrom. Rev., 16: 53, 1997.
Guan, S. and Marshall, A. G. Chem. Rev., 94: 2161, 1994
QIT
Marsh, R.E. et al., Quadrupole Storage Mass Spectrometry, vol.102, Wiley and Sons, New York, NY, 1989.
Cooks, R.G. et al., Ion trap mass spectrometry. Chem. Eng. News, 69(12): 26, 1991.
Jonscher, K.R. et al., Anal Biochem, 244(1): 1, 1997.
Louris, J.N. et al., Anal. Chem., 59(13): 1677, 1987.
Louris, J.N. et al., Int. J. Mass Spectrom. Ion Processes, 96(2): 117 1990.
Cooks, R.G. et al., Int. J. Mass Spectrom. Ion Processes, 118-119: 1 1992.
McLuckey, S. A. et al., Int. J. Mass Spectrom. Ion Processes, 106: 213, 1991.
Ngoka, L. C. M. and Gross, M. L. Int. J. Mass Spectrom. 194: 247, 2000.
69
Suggested Reading List
QQQ
Yost, R. A. and Enke, C. G. J. Am. Chem. Soc., 100: 2274, 1978.
Arnott, D. in Proteome Research: Mass Spectrometry, james, P (Ed.), pp 11-31, Springer-Verlag, Germany, 2001.
Steen H. et al., JMS, 36: 782, 2001
Miller, P.E. and Denton, M.B., J. Chem. Educ., 7: 617, 1986.
Yang, l. et al., Rapid Commun. Mass Spectrom., 16(21): 2060, 2002.
Mohammed, S. et al., JMS, 36: 1260, 2001.
Dongre, A.R. et al., JMS, 31: 339, 1996.
Orbitrap
Hu, Q, Noll, RJ, Li, H., Makarov, A., Hardman, M., Cooks, R.G. JMS, 430-443, 2005.
Makarov A. Anal. Chem. 2000; 72(6):1156-1162.
Makarov A, Denisov E, Kholomeev A, Baischun W, Lange O, Strupat K, Anal. Chem. 2006; 78(7):2113-2120.
Makarov A, Denisov E, Lange O, Horning S. JASMS. 2006; 17(7):977-982.
Macek B, Waanders LF, Olsen JV, Mann M. Mol. Cell. Proteom. 2006; 5(5):949-958.
Perry RH, Cooks RG, Noll RJ. Mass Spectrom. Rev. 2008; 27(6):661-699.
Scigelova M, Makarov A. Orbitrap mass analyzer - Overview and applications in proteomics. Proteomics. 2006: 1621.
Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M. Nature Methods. 2007; 4(9):709-712.
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