Due to unexpected PTMs, mutations, contaminants and novel peptides, nearly every proteomics mass spectrometry experiment produces a large amount of high-quality spectra not matched by any database peptides. Identifying these "non-database" peptides is valuable in all proteomics research and is particularly important to applications in protein sequencing, antibody confirmation, and biomarker discovery.
The traditional database search alone is insufficient to identify these important "non-database" peptides. Instead, PEAKS employs four complementary algorithms for de novo sequencing, database search, PTMs, and mutations, respectively. Integrating these algorithms maximizes the search sensitivity and the coverage of both the MS/MS data and the studied proteins.
PEAKS seamlessly integrates these four algorithms into its default search workflow. This workflow allows users to select which algorithms to turn on simply by checking a check box.
After the analysis, all the identified peptides (together with mutations, PTMs, and matched de novo tags) are aligned together in a protein coverage view. The coverage pane provides a convenient way to profile every single amino acid of the protein. The protein coverage can be dynamically configured and exported to HTML for easy result reporting and sharing.