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X!Tandem MSMS Search (version 1.1.1)

Database source:

Uploaded FASTA file:

Baseline Parameters:

Paramset:

MSMS File:

A file with MS/MS data

Variable Modifications:

Hold the appropriate key while clicking to select multiple items

Custom Variable Modifications

Custom Variable Modifications 0

Fixed Modifications:

Hold the appropriate key while clicking to select multiple items

Custom Fixed Modifications

Custom Fixed Modifications 0

Allow N-terminal protein acetylation as a variable modification:

Missed Cleavages Allowed:

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

Allow semi-cleaved peptides:

This can increase search time dramatically

Keep Spectra:

Include spectra in the output

Enzyme:

Fragment ion tolerance:

Fragment Ion Tolerance in Daltons

Precursor ion tolerance:

Precursor Ion Tolerance (Da or ppm)

Precursor Ion Tolerance Units:

Allow multi-isotope search:

This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass.

What it does

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

References

Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.