The process of searching mass spectral data for the purpose of peptide and protein identification can roughly be divided into six steps:
- Convert the raw, typically binary, output from the MS instrument into open formats.
- Process the MS/MS spectra into peak lists.
- Retrieve the desired sequence database and adapt it to the identification strategy.
- Search the peak lists against a sequence database using one or more search engines.
- Identify the peptides and infer the proteins.
- Validate the detected peptides and proteins.
This chapter will guide you through all these steps:
- 1.1 Database Generation (pdf)
- 1.2 Peak List Generation (pdf) (resources) (tools)
- 1.3 Peptide to Spectrum Matching (pdf) (resources) (tools)
- 1.4 Browsing Identification Results (pdf) (resources) (tools)
- 1.5 Peptide and Protein Validation (pdf) (tools)
- 1.6 PTM Analysis (pdf) (resources) (tools)
- 1.7 De Novo Peptide Identification (pdf) (resources) (tools)
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