The process of searching mass spectral data for the purpose of peptide and protein identification can roughly be divided into six steps:

  1. Convert the raw, typically binary, output from the MS instrument into open formats.
  2. Process the MS/MS spectra into peak lists.
  3. Retrieve the desired sequence database and adapt it to the identification strategy.
  4. Search the peak lists against a sequence database using one or more search engines.
  5. Identify the peptides and infer the proteins.
  6. Validate the detected peptides and proteins.

This chapter will guide you through all these steps:

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