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


BACKGROUND
SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm


BACKGROUND
Supplementary data are available at Bioinformatics online.


BACKGROUND
vwysocki@email.arizona.edu.
Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
Wenzhou
W
Li
Heather A
HA
O'Neill
Vicki H
VH
Wysocki
D000465:Algorithms; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software; D014584:User-Computer Interface
D010455:Peptides