Proteomics Informatics – Overview of Mass spectrometry (Week 2) Ion Source Mass Analyzer Detector mass/charge intensity.

Proteomics Informatics – Overview of Mass spectrometry (Week 2)

Ion Source

Mass Analyzer

Detector

mass/charge

inte

nsi

ty

Peptide FragmentationMass

Analyzer 1Frag-

mentationDetector

Ion Source

Mass Analyzer 2

b

y

Liquid Chromatography (LC)-MS/MS

Mass Analyzer 1

Frag-mentation

Detector

inte

ns

ity

mass/charge

Ion Source

Mass Analyzer 2

LC

inte

ns

ity

mass/chargeinte

ns

ity

mass/charge

inte

ns

ity

mass/chargeinte

ns

ity

mass/chargeinte

ns

ity

mass/charge

Time

inte

ns

ity

mass/chargeinte

ns

ity

mass/chargeinte

ns

ity

mass/charge

inte

ns

ity

mass/chargeinte

ns

ity

mass/chargeinte

ns

ity

mass/charge

inte

ns

ity

mass/chargeinte

ns

ity

mass/chargeinte

ns

ity

mass/charge

Ion Sources

Ion Source

Mass Analyzer

Detector

MALDIESI

mass/charge

inte

nsi

ty

Electrospray

Mass Analyzer

Detector

Matrix Assisted Laser Desorption Ionization (MALDI)

alpha-cyano-4-hydroxycinnamic acid

Matrix

Laser

V

Mass Analyzer

Detector

Detectors

Ion Source

Mass Analyzer

Detector

mass/charge

inte

nsi

tyElectron Multiplier

Image 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

nsi

ty

Mass Spectrometry (MS)

)( BvEzdt

vdmamF

BvEdt

vd

z

m

Time-of-Flight Mass Spectrometry

Ion Source

Mass Analyzer

Detector

Time-of-Flight

Detector

Detec

tor

Ion mirror

vtL

zV mv

2

2

L

z

m

V

Lt

2

V

Magnetic Sector

2

2

2

mv

mv

zV

zvBR

F

B

V

z

mR

2

Quadrupole Mass Filter

y

x

)cos( tVU

)cos( tVU

Ion Trap

Fourier transform ion cyclotron resonance

zvBR

F mv 2

B

Bv

R

z

m

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

ten

sity

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

time

m/z

time

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

nsi

ty1. MS2. MS/MS 13. MS/MS 24. MS/MS 3

mass/charge

inte

nsi

ty

mass/charge

inte

nsi

tyin

ten

sity

mass/charge

inte

nsi

ty

mass/charge

mass/charge

inte

nsi

ty

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

nsi

ty

mass/charge

inte

nsi

ty12. 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

nsi

ty

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

nsi

ty

700

0

D:\Users\Fenyo\Desktop\ATP.txt (15:46 02/03/11)Description: none available

m/z1300 1460In

ten

sity

45

0

D:\Users\Fenyo\Desktop\ATP.txt (15:50 02/03/11)Description: none available

m/z1444.0 1458.0

Inte

nsi

ty

35

0

D:\Users\Fenyo\Desktop\ATP.txt (15:54 02/03/11)Description: none available

m/z2378.0 2394.0

Inte

nsi

ty

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

ela

tive

Ab

un

da

nce

100

0250 500 750 1000

[M+2H]2+

762

260 389 504

633

875

292405 534

9071020663 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

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

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

nsi

ty