Percolator Results

Output from Percolator is in tab-delimited ASCII text. The results can be viewed in spreadsheet software. Standard output contains PSMs unique by peptide sequence (including modifications) and all redundancies are removed (e.g. alternative charge states are not represented). It is possible to alter the contents and representation of the results via command line options when running Percolator; however, these alternatives are beyond the scope of this documentation. Below are descriptions for the Percolator output.

Validated PSM Information

Result Description
PSMId Unique identifier that contains tracking information (input file name, scan number, retention time) to cross-reference the Percolator result with the original Kojak result.
score A Percolator-specific score representation of the PSM. This value has no relation to the Kojak score.
q-value The value that is used to determine a false discovery rate threshold. For example, a 1% FDR threshold would accept all PSMs with a q-value of 0.01 or less.
posterior_error_prob This value is the probability that the PSM is a false positive. Lower numbers are better.
peptide The unique PSM sequence. Cross-linked peptides are separated with a double dash, '--'. The sites of linkage are represented in parentheses after each peptide. For loop-links, both sites are represented with a single set of parentheses. Modification masses (other than the cross-linker) are represented inside square brackets, '[]', after the amino acid that contains them. Modifications include mono-linked representations of the chemical cross-linker.
proteinIds All proteins represented by the peptide(s) in the previous field are tab-delimited for the remainder of the line. The order of the proteins is alphabetic, and thus does not reflect the order of the peptides represented in cross-links.

Additional Information

Percolator represents proteins in alphabetical order. Thus, the proteins are not listed in the same order as the peptides in a cross-link. The proper peptide-protein associations can be cross-referenced in the Kojak results.

If decoy labels appear in the Percolator results it is either because the peptide sequence is shared between target and decoy protein sequences, or the decoy_filter label was not set properly during Kojak analysis.