MaxQuant enables high peptide identification rates, individual-ized p.p.b.-range mass accura-cies and proteome-wide protein

quantificationYoona Kim

University of California, San Diego

UCSD Mass Spectrometry Journal Club 12/03/10

MaxQuant

What is the MaxQuant? What’s benefits from MaxQuant? Conclusion Critisism

Outline

Input : High resolution, quantitative MS data of SILAC-en-coded cell populations

MaxQuant

Output: Identified MS/MS spectra and protein quantification graph(x=protein ration/y=intensity)

What is the MaxQuant?

Stable amino acid isotope-la-beled (SILAC) (1)

Stable amino acid iso-tope-labeled (SILAC) (2)

4. Visualization

3. Identification and validation

2. MS/MS Ion search - Mascot

1. Feature detection and peptide quantitation

MaxQuant’s pipeline

2D peaks

1. Feature detection and peptide quantitation-Peak Detection (1)

3D peaks

A bootstrap estimation over B = 150∵unknown atomic composition and intensity profiles overlap

1. Feature detection and peptide quantitation-Peak Detection (2)

Step 1: All possible pairs of isotope patterns- The correlation test >0.5- Have equal charge, close enough in mass

Step 2 : Convolute two isotope patterns- K, R, KK, KR, RR, KKK, KKR, KRR, and RRR- Find the same atomic composition

1. Feature detection and peptide quantitation-SILAC pair detection (1)

Ex. The peptide contains one K and no R- Heavy isotope labeled form ,

1. Feature detection and peptide quantitation-SILAC pair detection (2)

1. Feature detection and peptide quantitation-SILAC pair detection (3)

Posterior Error Probability - for calculating the false-discovery rate

3. Identification and validation

3. Identification and validation–Peptide score distributions

1. Improving peptide mass accu-racy

2. High rate of identified MS/MS spectra

3. Proteome-wide protein quantifiation

What’s the benefits from MaxQuant?

1. Improving peptide mass ac-curacy

2. High rate of identified MS/MS spectra

Protein ratio = median(all SILAC peptide ra-tio)

P-value for detection of significant outlier ratio (significance A)

3. Proteome-wide protein quan-tifiation

3. Proteome-wide protein quan-tifiation

Significance A Significance B

MaxQuant improves◦ Peptide identification rates◦ Peptide mass accuracy◦ Proteom-wide protein quantification

Conclusion

All experimental results are based on Mas-cot search◦ Mascot does not fully benefit from high-accuracy

(limit 0.25Da)

-> It is not working…!! (Sangtae said)

Critisism

IF you have more ques-tions…..

Go MaxQunt summer schoolIt will be fun!!!