Proteomics Informatics –
Overview of Mass spectrometry (Week 2)
Mass
Analyzer
intensity
Ion
Source
mass/charge
Detector
Peptide Fragmentation
Mass
Analyzer 1
Ion Source
Fragmentation
Mass
Analyzer 2
Detector
b
y
Liquid Chromatography (LC)-MS/MS
LC
Ion Source
mass/charge
mass/charge
Detector
mass/charge
mass/charge
mass/charge
Time
intensity
intensity
intensity
mass/charge
Mass
Analyzer 2
intensity
mass/charge
mass/charge
intensity
mass/charge
intensity
mass/charge
intensity
mass/charge
Fragmentation
intensity
intensity
intensity
mass/charge
intensity
intensity
intensity
intensity
intensity
Mass
Analyzer 1
mass/charge
mass/charge
mass/charge
Ion Sources
Ion
Source
Mass
Analyzer
intensity
MALDI
ESI
mass/charge
Detector
Electrospray
Mass
Analyzer
Detector
Matrix Assisted Laser Desorption Ionization
(MALDI)
Mass
Analyzer
Detector
V
Laser
Matrix
alpha-cyano-4-hydroxycinnamic acid
Detectors
Ion
Source
Mass
Analyzer
Detector
intensity
Electron Multiplier
Image Current
mass/charge
Electron Multiplier Detector
Image Current Detector
Mass Analyzers
Ion
Source
Mass
Analyzer
intensity
Time-of-Flight
Magnetic Sector
Quadrupole
Ion Trap (3D, linear)
FTICR
Orbitrap
mass/charge
Detector
Mass Spectrometry (MS)
F  ma  m
dv
 z(E  v  B)
dt
m dv
z dt
 E  v B
Time-of-Flight Mass Spectrometry
Ion
Source
zV 
mv
2
Mass
Analyzer
Detector
Time-of-Flight
L
2
L  vt
Detector
t
L
m
2V
z
V
Magnetic Sector
F 
mv
2
 zvB
R
zV 
mv
2
2
R 
m
2V
z
B
Quadrupole Mass Filter
y
 U  V cos(  t )
x
U  V cos(  t )
Ion Trap
Fourier transform ion cyclotron resonance
F 
mv
2
 zvB
R
m
z

R
v
B 
B

Orbitrap
Quadrupole Time-of-Flight Mass Spectrometer
Ion Source
Detector
CAD – Collision
Activated
Dissociation
Mass
Analyzer 1
Quadrupole
Video
Fragmentation
Mass
Analyzer 2
Time-of-Flight
Triple Quadrupole
Ion Source
Detector
CAD – Collision
Activated
Dissociation
Quadrupole
Quadrupole
time
m/z
m/z
time
time
YES
time
Dm/z is constant
m/z
YES
time
time
mass/charge
m/z
time
m/z
m/z
time
NO
m/z
Quadrupole
intensity
Mass
Analyzer 2
m/z
Fragmentation
m/z
Mass
Analyzer 1
time
Linear Ion Trap / Orbitrap
ESI
Linear Ion Trap
HCD
Ion
Source
Mass
Analyzer 1
Fragmentation
Detector
CAD
ETD
Fragmentation
Mass
Analyzer 2
Detector
Orbitrap
Olsen J V et al. Mol Cell Proteomics 2009;8:2759-2769
Video
intensity
intensity
intensity
mass/charge
mass/charge
intensity
mass/charge
mass/charge
intensity
1. MS
2. MS/MS 1
3. MS/MS 2
4. MS/MS 3
5. MS
6. MS/MS 1
7. MS/MS 2
8. MS/MS 3
9. MS
10. MS/MS 1
11. MS/MS 2
12. MS/MS 3
13. MS
14. MS/MS 1
15. MS/MS 2
16. MS/MS 3
17. MS
18. MS/MS 1
19. MS/MS 2
20. MS/MS 3
21. MS
22. MS/MS 1
23. MS/MS 2
24. MS/MS 3
…
intensity
Data Independent Acquisistion
mass/charge
mass/charge
MS
MS/MS 1
MS/MS 2
MS/MS 3
MS/MS 4
MS/MS 5
MS/MS 6
MS/MS 7
MS/MS 8
MS/MS 9
MS/MS 10
12. MS
13. MS/MS 1
14. MS/MS 2
15. MS/MS 3
16. MS/MS 4
17. MS/MS 5
18. MS/MS 6
19. MS/MS 7
20. MS/MS 8
21. MS/MS 9
22. MS/MS 10
…
mass/charge
intensity
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
intensity
Data Dependent Acquisistion
mass/charge
Vacuum System
Vacuum System
Ion
Source
Atmosphere
Mass
Analyzer
Detector
Mass Spectrometry Data
Mass
Analyzer
intensity
Ion
Source
mass/charge
Detector
Mass Spectrometry Data
Dimensions:
Time
Peptide m/z
Peptide Intensity
Petide fragment m/z
Peptide fragment intensity
...
Example data – MALDI-TOF
45
700
Intensity
Intensity
1800
0
1000
D:\Users\Fenyo\Desktop\ATP.txt (15:42 02/03/11)
Description: none available
4500
m/z
0
1300
2280
14602400
m/z
D:\Users\Fenyo\Desktop\ATP.txt (15:50
(15:4602/03/11)
Description: none available
Peptide intensity vs m/z
Intensity
700
35
0
2378.0
1444.0
m/z
2394.0
1458.0
Example data – ESI-LC-MS/MS
m/z
Peptide intensity vs m/z vs time
762
MS/MS
% Relative Abundance
100
0
Time
875
[M+2H]2+
292
405
534
260
389
504
250
500
633
663
m/z
778
750
1022
9071020 1080
1000
Fragment intensity vs m/z
Slice - Scalable Data Sharing for
Remote Mass Informatics
Developed by Manor Askenazi
slice.ionomix.com
Most mass spectrometry data is acquired in discovery mode, meaning
that the data is amenable to open-ended analysis as our understanding
of the target biochemistry increases. In this sense, mass
spectrometry based discovery work is more akin to an astronomical
survey, where the full list of object-types being imaged has not yet
been fully elucidated, as opposed to e.g. micro-array work, where the
list of probes spotted onto the slide is finite and well understood.
Example Mass Spectrometry Data
fenyolab.ionomix.com
Example Mass Spectrometry Data
Peptide intensity vs time
For 737.707 m/z which corresponds to
3+ of LGEHNIDVLEGNEQFINAAK
Example Mass Spectrometry Data
Fragment intensity vs m/z
For 3+ of LGEHNIDVLEGNEQFINAAK
Example Mass Spectrometry Data
Fragment intensity vs m/z
For 3+ of LGEHNIDVLEGNEQFINAAK
Example Mass Spectrometry Data
3+ of LGEHNIDVLEGNEQFINAAK
Peptide intensity vs m/z
Example Mass Spectrometry Data
3+ of LGEHNIDVLEGNEQFINAAK
Peptide intensity vs m/z
Example Mass Spectrometry Data
Peptide intensity vs m/z
Peptide intensity vs time
Example Mass Spectrometry Data
ASTHTDSSAQTVSLEDYVSR 3+ in E. coli
DTTTIIDGVGEEAAIQGR 2+ in E. coli
ATGTSEMAPALVAAFGGK 2+ in E. coli
FVPDTQAPLGIR 2+ in E. coli
Proteomics Informatics –
Overview of Mass spectrometry (Week 2)
Mass
Analyzer
intensity
Ion
Source
mass/charge
Detector