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OMSSA MSMS Search (version 1.1.1)

Database source:

Uploaded FASTA file:

MSMS File:

An mgf file with MS/MS data

Variable Modifications:

Hold the appropriate key while clicking to select multiple items

Fixed Modifications:

Hold the appropriate key while clicking to select multiple items

Missed Cleavages Allowed:

Allow peptides to contain up to this many missed enzyme cleavage sites

Enzyme:

Fragment ion tolerance:

Fragment Ion Tolerance in Daltons

Maximum Expect value allowed in the hit list:

Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet

Peak intensity cut-off:

Peak intensity cut-off as a fraction of maximum peak intensity

Precursor ion tolerance:

Precursor Ion Tolerance (Da or ppm)

Precursor Ion Tolerance Units:

Use average precursor masses:

Match precursor to average mass of the parent ion instead of its monoisotopic mass

Respect precursor charges:

Use precursor charge information in input file rather than OMSSA's inferred value

Multi-isotope search.:

Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search

Ions included in search:

What it does

Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.

Citation

If you use this tool please read and cite the paper describing OMSSA.

Geer L. Y., et al. “Open mass spectrometry search algorithm” J. Proteome Res. 3(5), 958-964 (2004).