PgxSAVy Help

PgxSAVy rescoring:

PgxSAVy require variant and spectra input file for rescoring analysis. A sample input and spectra file can be downloaded here: Variant input and Spectra input.

Variant Input File:

Variant input can be in either tab separated format, MSGF tsv converted format or EuGenoSuite output format.

The tab separated format should contains following columns:

  1. Scan ID
  2. Variant Peptide
  3. Wildtype Peptide
  4. Variants
  5. Variant Amino Acid
  6. Wildtype Amino Acid
  7. Variant Position
  8. Protein Position
  9. Protein ID
  10. Modifications
  11. Charge
  12. Search engine counts
Spectra Input File:

Spectra input file should be in MGF format. If other format, then convert it to MGF format using MSConvert tool.

PgxSAVy disease annotation:

PgxSAVy perform annotation of variant peptides using UniProt variant information. Current variant information version integrated in PgxSAVy is November 2023. The latest UniProt variant information can be downloaded from UniProt FTP link.