Computational Biology

Volume 673 of the series Methods in Molecular Biology pp 189-202


Mass Spectrometric Protein Identification Using the Global Proteome Machine

  • David FenyöAffiliated withThe Rockefeller University Email author 
  • , Jan ErikssonAffiliated withDepartment of Chemistry, Swedish University of Agricultural Sciences
  • , Ronald BeavisAffiliated withThe Biomedical Research Centre, University of British Columbia

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Protein identification by mass spectrometry is widely used in biological research. Here, we describe how the global proteome machine (GPM) can be used for protein identification and for validation of the results. We cover identification by searching protein sequence collections and spectral libraries as well as validation of the results using expectation values, rho-diagrams, and spectrum databases.

Key words

Proteomics Mass spectrometry Protein identification Spectrum libraries Validation