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Protein Identification with Mascot Software. (Laxmana Rao Y. and Gopalacharyulu P.V.). Protein extract from Biological sample. MALDI ESI. QTof FTMS . . . . Protein Identification. Proteomics & Mass Spectrometry. 337 nm UV laser. cyano-hydroxy cinnamic acid. MRNSYRFLASSL

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protein identification with mascot software

Protein Identification with Mascot Software

(Laxmana Rao Y. and Gopalacharyulu P.V.)

proteomics mass spectrometry

Protein extract from

Biological sample

MALDI

ESI

QTof

FTMS

. . .

Protein Identification

Proteomics & Mass Spectrometry
peptide mass fingerprinting

337 nm UV laser

cyano-hydroxy

cinnamic acid

MRNSYRFLASSL

SVVVSLLLIPED

VCEKIIGGNEVT

PHSRPYMVLLSL

DRKTICAGALIA

KDWVLTAAHCNL

NKRSQVILGAHS

ITYEEPTKQIML

VKKEFPYPCYDP

ATREGDLKLLQL

100

100

LASSLSVVVSLLLIPEDVCEK

IIGGNEVTPHSR

PYMVLLSLDR

TICAGALIAK

DWVLTAAHCNLNKR

ITTTYEEPTK

QIMLVK

EFPYPCYDPATR

EGDLKLL

80

80

60

60

%TIC

%TIC

40

40

20

20

0

0

m/z

m/z

Protein Database

In Silico Digestion

Peptide Mass Fingerprinting

Complex Protein Mixture

Purified Protein

2D Gel Separation

Peptide Digest

MALDI

Proteolysis

Mass Spec

Theoretical MS

Experimental MS

ms ms fragment ion analysis

In Silico

Digestion

In Silico

Fragmentation

Protein Database

100

MRNSYRFLASSL

SVVVSLLLIPED

VCEKIIGGNEVT

PHSRPYMVLLSL

DRKTICAGALIA

KDWVLTAAHCNL

NKRSQVILGAHS

ITYEEPTKQIML

VKKEFPYPCYDP

ATREGDLKLLQL

100

80

LASSLSVVVSLLCEK

IIGGNEVTPHSR

PYMVLLSLDR

TICAGALIAK

DWVLTAAHCNLNKR

ITTTYEEPTK

QIMLVK

EFPYPCYDPATR

EGDLKLL

P YMVLLSLDR

PYM VLLSLDR

PYMV LLSLDR

PYMVL LSLDR

PYMVLL SLDR

PYMVLLS LDR

PYMVLLSL DR

PYVLLSLD MR

PYMVLLSLD R

80

60

%TIC

60

%TIC

40

40

20

20

0

0

m/z

m/z

MS/MS Fragment Ion Analysis

Complex Protein Mixture

Peptide Digest

Proteolysis

HPLC

MS/MS

Theoretical

Fragmentation

Spectrum

Experimental

Fragmentation

Spectrum

mascot scoring
Mascot Scoring
  • The Mascot Score is given as S = -10*Log(P), where P is the probability that the observed match is a random event
  • The significance of that result depends on the size of the database being searched. Mascot shades in green the insignificant hits using a P=0.05 cutoff.

In this example,

scores less than 74 are

insignificant

Mascot Score:

120 = 1x10-12

pmf results
PMF: Results

Results will be explained in more detail

in a live-web demo at the end of the

presentation

ms ms ions search results
MS/MS Ions Search: Results

Results will be explained in more detail

in a live-web demo at the end of the

presentation

mascot sequence query result
Mascot Sequence Query: Result

Results will be explained in more detail

in a live-web demo at the end of the

presentation