Introduction

Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using >600,000 peptide identifications generated by four proteomic platforms, we empirically identified >16,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with >85% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation).

Publications

  1. Computational prediction of proteotypic peptides for quantitative proteomics.
    Cite this
    Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R, 2007-01-01 - Nature biotechnology

Credits

  1. Parag Mallick
    Developer

  2. Markus Schirle
    Developer

  3. Sharon S Chen
    Developer

  4. Mark R Flory
    Developer

  5. Hookeun Lee
    Developer

  6. Daniel Martin
    Developer

  7. Jeffrey Ranish
    Developer

  8. Brian Raught
    Developer

  9. Robert Schmitt
    Developer

  10. Thilo Werner
    Developer

  11. Bernhard Kuster
    Developer

  12. Ruedi Aebersold
    Investigator

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Summary
AccessionBT005385
Tool TypeApplication
Category
PlatformsWindows
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByRuedi Aebersold