proteomics informatics – overview of mass spectrometry (week 2)
DESCRIPTION
Proteomics Informatics – Overview of Mass spectrometry (Week 2). Ion Source. Mass Analyzer. Detector. intensity. mass/charge. Peptide Fragmentation. b. Ion Source. Mass Analyzer 1. Frag-mentation. Mass Analyzer 2. Detector. y. Liquid Chromatography (LC)-MS/MS. LC. Ion Source. - PowerPoint PPT PresentationTRANSCRIPT
Proteomics Informatics – Overview of Mass spectrometry (Week 2)
Ion Source
Mass Analyzer Detector
mass/charge
inte
nsity
Peptide FragmentationMass
Analyzer 1Frag-
mentation DetectorIon Source
Mass Analyzer 2
b
y
Liquid Chromatography (LC)-MS/MS
Mass Analyzer 1
Frag-mentation
Detector
inte
nsity
mass/charge
Ion Source
Mass Analyzer 2
LC
inte
nsity
mass/chargeinte
nsity
mass/charge
inte
nsity
mass/chargeinte
nsity
mass/chargeinte
nsity
mass/charge
Time
inte
nsity
mass/chargeinte
nsity
mass/chargeinte
nsity
mass/charge
inte
nsity
mass/chargeinte
nsity
mass/chargeinte
nsity
mass/charge
inte
nsity
mass/chargeinte
nsity
mass/chargeinte
nsity
mass/charge
Ion Sources
Ion Source
Mass Analyzer Detector
MALDIESI
mass/charge
inte
nsity
Electrospray
Mass Analyzer Detector
Matrix Assisted Laser Desorption Ionization (MALDI)
alpha-cyano-4-hydroxycinnamic acid
MatrixLaser
V
Mass Analyzer Detector
Detectors
Ion Source
Mass Analyzer Detector
mass/charge
inte
nsity
Electron MultiplierImage Current
Electron Multiplier Detector
Image Current Detector
Mass Analyzers
Ion Source
Mass Analyzer Detector
Time-of-FlightMagnetic Sector
QuadrupoleIon Trap (3D, linear)
FTICROrbitrap
mass/charge
inte
nsity
Mass Spectrometry (MS)
)( BvEzdtvdmamF
BvEdtvd
zm
Time-of-Flight Mass SpectrometryIon
SourceMass
Analyzer Detector
Time-of-Flight
Detector
Detecto
r
Ion mirror
vtL
zV mv
2
2
L
zm
VLt2
V
Magnetic Sector
2
2
2
mv
mv
zV
zvBR
F
BV
zmR 2
Quadrupole Mass Filter
y
x)cos( tVU
)cos( tVU
Ion Trap
Fourier transform ion cyclotron resonance
zvBR
F mv 2
BB
vR
zm
Orbitrap
Quadrupole Time-of-Flight Mass Spectrometer
Video
Mass Analyzer 1
Frag-mentation
DetectorIon Source
Mass Analyzer 2
CAD – Collision Activated
Dissociation
Quadrupole Time-of-Flight
Triple Quadrupole
Mass Analyzer 1
Frag-mentation
Detector
mass/chargein
tens
ity
Ion Source
Mass Analyzer 2
CAD – Collision Activated
Dissociation
Quadrupole Quadrupole Quadrupole
time
m/z
time
m/z
time
m/z
time
m/z
time
m/z
time
m/z
NO
YES
timem
/ztime
m/z YESm/z
timeDm/z is constant
Linear Ion Trap / Orbitrap
Mass Analyzer 1
Frag-mentation
Detector
Ion Source
Mass Analyzer 2
ESI Linear Ion Trap
Orbitrap
CADETD
Olsen J V et al. Mol Cell Proteomics 2009;8:2759-2769
Frag-mentation
HCD
Detector
Video
Data Independent Acquisistion
mass/charge
inte
nsity
1. MS2. MS/MS 13. MS/MS 24. MS/MS 3
mass/charge
inte
nsity
mass/chargein
tens
ityin
tens
ity
mass/charge
inte
nsity
mass/charge
mass/charge
inte
nsity
5. MS6. MS/MS 17. MS/MS 28. MS/MS 39. MS10. MS/MS 111. MS/MS 212. MS/MS 313. MS14. MS/MS 115. MS/MS 216. MS/MS 317. MS18. MS/MS 119. MS/MS 220. MS/MS 321. MS22. MS/MS 123. MS/MS 224. MS/MS 3…
1. MS2. MS/MS 13. MS/MS 24. MS/MS 35. MS/MS 46. MS/MS 57. MS/MS 68. MS/MS 79. MS/MS 810. MS/MS 911. MS/MS 10
Data Dependent Acquisistion
mass/charge
inte
nsity
mass/charge
inte
nsity
12. MS13. MS/MS 114. MS/MS 215. MS/MS 316. MS/MS 417. MS/MS 518. MS/MS 619. MS/MS 720. MS/MS 821. MS/MS 922. MS/MS 10…
Vacuum System
Ion Source
Mass Analyzer Detector
Vacuum System
Atmosphere
Mass Spectrometry Data
Ion Source
Mass Analyzer Detector
mass/charge
inte
nsity
Mass Spectrometry Data
Dimensions:
TimePeptide m/z
Peptide IntensityPetide fragment m/z
Peptide fragment intensity
...
Example data – MALDI-TOF
m/z1000 4500
Inte
nsity
1800
0
D:\Users\Fenyo\Desktop\ATP.txt (15:42 02/03/11)Description: none available m/z2280 2400
Inte
nsity
700
0
D:\Users\Fenyo\Desktop\ATP.txt (15:46 02/03/11)Description: none available
m/z1300 1460In
tens
ity
45
0
D:\Users\Fenyo\Desktop\ATP.txt (15:50 02/03/11)Description: none available
m/z1444.0 1458.0
Inte
nsity
35
0
D:\Users\Fenyo\Desktop\ATP.txt (15:54 02/03/11)Description: none available
m/z2378.0 2394.0
Inte
nsity
700
0
D:\Users\Fenyo\Desktop\ATP.txt (16:07 02/03/11)Description: none available
Peptide intensity vs m/z
Fragment intensity vs m/z
Example data – ESI-LC-MS/MS
Time
m/z
m/z
% R
elat
ive
Abu
ndan
ce100
0250 500 750 1000
[M+2H]2+
762
260 389 504
633
875
292 405 5349071020663 778 1080
1022
MS/MS
Peptide intensity vs m/z vs time
Slice - Scalable Data Sharing for Remote Mass Informatics
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.
slice.ionomix.comDeveloped by Manor Askenazi
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
Peptide intensity vs m/z
3+ of LGEHNIDVLEGNEQFINAAK
Example Mass Spectrometry Data
Peptide intensity vs m/z
3+ of LGEHNIDVLEGNEQFINAAK
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)
Ion Source
Mass Analyzer Detector
mass/charge
inte
nsity