{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:58:09Z","timestamp":1761541089901},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: SQID-XLink program is freely available for download from http:\/\/quiz2.chem.arizona.edu\/wysocki\/bioinformatics.htm<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0vwysocki@email.arizona.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts442","type":"journal-article","created":{"date-parts":[[2012,7,14]],"date-time":"2012-07-14T09:29:14Z","timestamp":1342258154000},"page":"2548-2550","source":"Crossref","is-referenced-by-count":9,"title":["SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification"],"prefix":"10.1093","volume":"28","author":[{"given":"Wenzhou","family":"Li","sequence":"first","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721 and 2Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA"}]},{"given":"Heather A.","family":"O\u2019Neill","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721 and 2Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA"}]},{"given":"Vicki H.","family":"Wysocki","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721 and 2Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,7,12]]},"reference":[{"key":"2023012513141148400_bts442-B1","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"TANDEM: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012513141148400_bts442-B2","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","article-title":"An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database","volume":"5","author":"Eng","year":"1994","journal-title":"J. Am. Soc. Mass Spectrom"},{"key":"2023012513141148400_bts442-B3","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1039\/b801810c","article-title":"Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes","volume":"4","author":"Lee","year":"2008","journal-title":"Mol. BioSyst."},{"key":"2023012513141148400_bts442-B4","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1021\/pr100959y","article-title":"SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry","volume":"10","author":"Li","year":"2011","journal-title":"J. Proteome Res."},{"key":"2023012513141148400_bts442-B5","doi-asserted-by":"crossref","first-page":"2200","DOI":"10.1074\/mcp.M700274-MCP200","article-title":"Structural analysis of multiprotein complexes by cross-linking, mass spectrometry, and database searching","volume":"6","author":"Maiolica","year":"2007","journal-title":"Mol Cell Proteomics."},{"key":"2023012513141148400_bts442-B6","doi-asserted-by":"crossref","first-page":"2488","DOI":"10.1021\/pr901163d","article-title":"Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs","volume":"9","author":"McIlwain","year":"2010","journal-title":"J Proteome Res."},{"key":"2023012513141148400_bts442-B7","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nmeth.1192","article-title":"Identification of cross-linked peptides from large sequence databases","volume":"5","author":"Rinner","year":"2008","journal-title":"Nat. Methods"},{"key":"2023012513141148400_bts442-B8","doi-asserted-by":"crossref","first-page":"8799","DOI":"10.1021\/ac801646f","article-title":"Characterization of protein cross-links via mass spectrometry and an open-modification search strategy","volume":"80","author":"Singh","year":"2008","journal-title":"Anal. Chem."},{"key":"2023012513141148400_bts442-B9","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1002\/jms.559","article-title":"Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes","volume":"38","author":"Sinz","year":"2003","journal-title":"J. Mass Spectrom."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/19\/2548\/48875143\/bioinformatics_28_19_2548.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/19\/2548\/48875143\/bioinformatics_28_19_2548.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:15:32Z","timestamp":1674674132000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/19\/2548\/288086"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,7,12]]},"references-count":9,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2012,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts442","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,10,1]]},"published":{"date-parts":[[2012,7,12]]}}}