biostudies-literatureLi WNIGMS NIH HHS2548-50https://www.ebi.ac.uk/biostudies/studies/S-EPMC3463113biostudies-literatureUnknown28(19)<h4>Summary</h4>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.<h4>Availability</h4>SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.<h4>Contact</h4>vwysocki@email.arizona.edu.Bioinformatics (Oxford, England)SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification.PMC34631132R01GM051387Li WWysocki VHO'Neill HAfalseSQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification.<h4>Summary</h4>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.<h4>Availability</h4>SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.<h4>Contact</h4>vwysocki@email.arizona.edu.2012-01-01T00:00:00Z2012 Oct2024-11-14T08:07:13.033Z2019-03-27T00:58:37ZS-EPMC34631132279695610.1093/bioinformatics/bts442