Kojak Results

Output from Kojak is in tab-delimited ASCII text. The first line of output indicates the Kojak version number that was used to generate the output. This line is followed by the column headers that describe the search results. The remainder of the file is populated by PSMs, one per line. Spectra for which no positive scoring PSM was identified will contain mostly zero values for each column. Occasionally, two or more PSMs will have the same score for a single spectrum. In these cases, all PSMs that share the same score are reported. For simplicity, column descriptions are divided into categories below.

Precursor Ion Information

Result Description
Charge Precursor ion charge state.
Obs Mass Observed mass of the precursor ion peak.
PPM Error Difference (in parts per million) between the PSM mass and the Obs Mass.
PSM Mass Theoretically computed precursor mass of the PSM.

Score Information

Result Description
Score The Kojak cross-correlation score.
dScore The difference between the reported PSM score and the next best PSM score.
Pep. Diff. The score contribution of only the lower scoring peptide in a cross-link.

Sequence Information

Result Description
Peptide #n The peptide sequence of the PSM. For cross-linked PSMs, a second sequence is provided as Peptide #2.
Link #n The site of cross-linking, relative to the peptide, . If the PSM is not a cross-link, a value of -1 is shown.
Protein #n The protein name(s) that contain the peptide. For cross-linked PSMs, a second list is provided as Protein #2. For cross-linked PSMs, the site of cross-linking relative to the protein is provided in parentheses.
Linker Mass The mass contribution of the cross-linker for cross-linked PSMs. Zero otherwise.