proteomics informatics – overview of mass spectrometry (week 2)

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

Openslice.fenyolab.org

Proteomics Informatics – Overview of Mass spectrometry (Week 2)

Ion Source

Mass Analyzer Detector

mass/charge

inte

nsity