The parameter can have the values yes or no.
When this value is set to yes, the protein sequences associated with a peptide-to-spectrum match are recorded in the XML output file. This is the recommended mode of operation for X! TANDEM, as it records the version of the protein sequence actually used for the identification. Sequence lists generated from database systems can change from time-to-time, with the deletion of accession numbers and the alteration of protein sequences associated with a particular accession number. If the output, proteins value is no, then this parameter is ignored.
If it is set to no, then these sequences are not recorded. The recording of the input parameters,performance statistics or other types of results are not affected by the value of this parameter.
see also: output, histograms | output, spectra | output, proteins
X! TANDEM API description project