SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification.

SUMMARY: Peptide identification algorithm is a major bottleneck for mass spectrometry based chemical cross-linking experiments. Our lab recently developed an intensity-incorporated peptide identification algorithm, and here we implemented this scheme for cross-linked peptide discovery. Our program, SQID-XLink, searches all regular, dead-end, intra and inter cross-linked peptides simultaneously, and its effectiveness is validated by testing a published dataset. This new algorithm provides an alternative approach for high confidence cross-linking identification. AVAILABILITY: SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: vwysocki@email.arizona.edu.