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X!Tandem (version 2.0.0)

select MS/MS input type:

MS/MS input file (mzml or mzxml):

precursor monoisotopic mass_tolerance_lower:

precursor monoisotopic mass_tolerance_upper:

precursor_error_units:

fragment_mass_tolerance:

fragment_error_units:

Protein sequences DB (FASTA):

Complete modifications:

Potential modifications:

minimum_fragment_mz:

cleavage_site:

maximum missed cleavage sites:

maximum number of missed cleavage sites allowed within a peptide. For a specific, aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate. For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate.

maximum valid expectation value:

Max E-Value of a hit to be reported. All results with expectation values less than this value are considered to be statisitically significant and are recorded.

Refine search:

Select this to enable a second round of more detailed searching, using only the set of proteins found by the contraints above. E.g. Rather than entering the 'potential modifications' in the options above, try entering them here only. This is faster and limits this more thorough searching to a set of proteins for which there is already some evidence.

Scoring, include reverse:

Use the X! Tandem protein sequence reverse method (sequences are reversed in memory and searched again, the tag ':reversed' is added to the protein description).

This tool searches MS/MS spectra against a database using X!Tandem.

For a complete set of parameters and their default values see the X!Tandem parameters documentation page . Parameters that are not made available in the UI above but are listed in the given link are submitted with their default values.

For more information on the refine step see: Why should I use "refinement" to find modifications? .

For more information on the expectation value calculation see: A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes , David Fenyö and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774. This reference describes how peptides are scored by X!Tandem. The expectation values on the individual peptides are calculated using this method.

Output

This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool.

It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match using an embedded spectrum viewer.

/repository/static/images/022e0bccbc85e62a/xtandem_results_viewer.png

Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this and do not need further processing steps like protein inference.

For the GPM web UI of X!Tandem see: http://ppp.thegpm.org/tandem/thegpm_ppp.html