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Yoona Kim University of California, San Diego

MaxQuant enables high peptide identification rates, individualized p.p.b. -range mass accuracies and proteome-wide protein quantification. Yoona Kim University of California, San Diego. UCSD Mass Spectrometry Journal Club 12/03/10. MaxQuant. Outline.

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Yoona Kim University of California, San Diego

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  1. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Yoona Kim University of California, San Diego UCSD Mass Spectrometry Journal Club 12/03/10

  2. MaxQuant

  3. Outline • What is the MaxQuant? • What’s benefits from MaxQuant? • Conclusion • Critisism

  4. What is the MaxQuant?

  5. Stable amino acid isotope-labeled (SILAC) (1)

  6. Stable amino acid isotope-labeled (SILAC) (2)

  7. MaxQuant’s pipeline

  8. 1. Feature detection and peptide quantitation-Peak Detection (1) • 2D peaks • 3D peaks

  9. 1. Feature detection and peptide quantitation-Peak Detection (2) • A bootstrap estimation over B = 150 ∵unknown atomic composition and intensity profiles overlap

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

  11. 1. Feature detection and peptide quantitation-SILAC pair detection (2) • Ex. The peptide contains one K and no R • Heavy isotope labeled form ,

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

  13. 3. Identification and validation • Posterior Error Probability - for calculating the false-discovery rate

  14. 3. Identification and validation–Peptide score distributions

  15. What’s the benefits from MaxQuant?

  16. 1. Improving peptide mass accuracy

  17. 2. High rate of identified MS/MS spectra

  18. 3. Proteome-wide protein quantifiation • Protein ratio = median(all SILAC peptide ratio) • P-value for detection of significant outlier ratio (significance A)

  19. 3. Proteome-wide protein quantifiation Significance A Significance B

  20. Conclusion • MaxQuant improves • Peptide identification rates • Peptide mass accuracy • Proteom-wide protein quantification

  21. Critisism • All experimental results are based on Mascot search • Mascot does not fully benefit from high-accuracy (limit 0.25Da) -> It is not working…!! (Sangtae said)

  22. IF you have more questions….. Go MaxQunt summer school It will be fun!!!

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