Introduction

The Open Mass Spectrometry Search Algorithm OMSSA is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. OMSSA is free and in the public domain. Detailed information can be found at http://pubchem.ncbi.nlm.nih.gov/omssa/.

Currently, the OMSSA-csv DAO supports spectra in PKL, DTA, MGF, MZXML, MS2, and MZML formats.

Parameters

• Threshold: The maximum expect value a peptide may have to still be included in the PRIDE XML file. All peptides with an expect value greater than the set threshold will be ignored. Default value is 0.0.

• Score Criteria: the score criteria used to apply the Threshold filter. Default value is E-value.

• Fixed PTMs: a user defined collection of fixed PTMs in the format delta-value@aminoacid and comma separated. Default list contains 57.02@C.

• Variable PTMs: a user defined collection of fixed PTMs in the format delta-value@aminoacid and comma separated. Default list contains 15.99@M.