Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing

Authors

  • You Li,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    2. Graduate University of Chinese Academy of Sciences, Beijing 100049, China
    Search for more papers by this author
    • These authors contributed equally to this work.

  • Hao Chi,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    2. Graduate University of Chinese Academy of Sciences, Beijing 100049, China
    Search for more papers by this author
    • These authors contributed equally to this work.

  • Le-Heng Wang,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    Search for more papers by this author
  • Hai-Peng Wang,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    2. Graduate University of Chinese Academy of Sciences, Beijing 100049, China
    Search for more papers by this author
  • Yan Fu,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    Search for more papers by this author
  • Zuo-Fei Yuan,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    2. Graduate University of Chinese Academy of Sciences, Beijing 100049, China
    Search for more papers by this author
  • Su-Jun Li,

    1. Research Center for Proteome Analysis, Key Lab of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Search for more papers by this author
  • Yan-Sheng Liu,

    1. Research Center for Proteome Analysis, Key Lab of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Search for more papers by this author
  • Rui-Xiang Sun,

    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    Search for more papers by this author
  • Rong Zeng,

    1. Research Center for Proteome Analysis, Key Lab of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Search for more papers by this author
  • Si-Min He

    Corresponding author
    1. Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    • Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
    Search for more papers by this author

Abstract

Database searching is the technique of choice for shotgun proteomics, and to date much research effort has been spent on improving its effectiveness. However, database searching faces a serious challenge of efficiency, considering the large numbers of mass spectra and the ever fast increase in peptide databases resulting from genome translations, enzymatic digestions, and post-translational modifications. In this study, we conducted systematic research on speeding up database search engines for protein identification and illustrate the key points with the specific design of the pFind 2.1 search engine as a running example. Firstly, by constructing peptide indexes, pFind achieves a speedup of two to three compared with that without peptide indexes. Secondly, by constructing indexes for observed precursor and fragment ions, pFind achieves another speedup of two. As a result, pFind compares very favorably with predominant search engines such as Mascot, SEQUEST and X!Tandem. Copyright © 2010 John Wiley & Sons, Ltd.

Ancillary