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Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

  • Zengyou He
  • Chao Yang
  • Can Yang
  • Robert Z. Qi
  • Jason Po-Ming Tam
  • Weichuan Yu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)

Abstract

In current proteome research, the most widely used method for protein mixture identification is probably peptide sequencing. Peptide sequencing is based on tandem Mass Spectrometry (MS/MS) data. The disadvantage is that MS/MS data only sequences a limited number of peptides and leaves many more peptides uncovered.

Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins from single-stage MS data. Unfortunately, this technique is less accurate than the peptide sequencing method and can not handle protein mixtures, which hampers the widespread use of PMF.

In this paper, we tackle the problem of protein mixture identification from an optimization point of view. We show that some simple heuristics can find good solutions to the optimization problem. As a result, we obtain much better identification results than previous methods. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF-based protein mixture identification. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures, especially in the identification of low-abundance proteins which are less likely to be sequenced by MS/MS scanning.

Availability: The source codes, data and supplementary documents are available at http://bioinformatics.ust.hk/PMFMixture.rar

Keywords

Sequence Coverage Single Protein Protein Mixture Mass Error Peptide Mass Fingerprint 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Zengyou He
    • 1
  • Chao Yang
    • 1
  • Can Yang
    • 1
  • Robert Z. Qi
    • 2
  • Jason Po-Ming Tam
    • 2
  • Weichuan Yu
    • 1
  1. 1.Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer EngineeringHong Kong
  2. 2.Department of BiochemistryThe Hong Kong University of Science and TechnologyHong KongChina

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