Introduction

Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration.We develop a Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar experimental conditions. Our method, MSpresso, substantially increases the number of proteins identified in an MS/MS experiment at the same error rate, e.g. in yeast, MSpresso increases the number of proteins identified by approximately 40%. We apply MSpresso to data from different MS/MS instruments, experimental conditions and organisms (Escherichia coli, human), and predict 19-63% more proteins across the different datasets. MSpresso demonstrates that incorporating prior knowledge of protein presence into shotgun proteomics experiments can substantially improve protein identification scores.Software is available upon request from the authors. Mass spectrometry datasets and supplementary information are available from (http://www.marcottelab.org/MSpresso/).

Publications

  1. Integrating shotgun proteomics and mRNA expression data to improve protein identification.
    Cite this
    Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R, 2009-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Smriti R Ramakrishnan
    Developer

    Department of Computer Sciences, The University of Texas at Austin, United States of America

  2. Christine Vogel
    Developer

  3. John T Prince
    Developer

  4. Zhihua Li
    Developer

  5. Luiz O Penalva
    Developer

  6. Margaret Myers
    Developer

  7. Edward M Marcotte
    Developer

  8. Daniel P Miranker
    Developer

  9. Rong Wang
    Investigator

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Summary
AccessionBT006839
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByRong Wang