{"id":"https://openalex.org/W2169467883","doi":"https://doi.org/10.1093/bioinformatics/bts442","title":"SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification","display_name":"SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification","publication_year":2012,"publication_date":"2012-07-12","ids":{"openalex":"https://openalex.org/W2169467883","doi":"https://doi.org/10.1093/bioinformatics/bts442","mag":"2169467883","pmid":"https://pubmed.ncbi.nlm.nih.gov/22796956"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/19/2548/13833702/bts442.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/19/2548/13833702/bts442.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102846425","display_name":"Wenzhou Li","orcid":"https://orcid.org/0000-0003-2506-6324"},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]},{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenzhou Li","raw_affiliation_strings":["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"],"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I138006243","https://openalex.org/I24603500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070357958","display_name":"Heather A. O\u2019Neill","orcid":null},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]},{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heather A. O\u2019Neill","raw_affiliation_strings":["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"],"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I138006243","https://openalex.org/I24603500"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054298903","display_name":"Vicki H. Wysocki","orcid":"https://orcid.org/0000-0003-0495-2538"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]},{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vicki H. Wysocki","raw_affiliation_strings":["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"],"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I138006243","https://openalex.org/I24603500"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054298903"],"corresponding_institution_ids":["https://openalex.org/I138006243","https://openalex.org/I24603500"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1305,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.75788886,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"19","first_page":"2548","last_page":"2550"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7411624193191528},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.6999038457870483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6083396077156067},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5269100069999695},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.46176356077194214},{"id":"https://openalex.org/keywords/scheme","display_name":"Scheme (mathematics)","score":0.44202202558517456},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4139624834060669},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34310680627822876},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17856597900390625},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1677599847316742},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1159694492816925}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7411624193191528},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.6999038457870483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6083396077156067},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5269100069999695},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.46176356077194214},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.44202202558517456},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4139624834060669},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34310680627822876},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17856597900390625},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1677599847316742},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1159694492816925},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/19/2548/13833702/bts442.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22796956","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22796956","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:2774919","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3463113","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/19/2548/13833702/bts442.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6658733114","display_name":null,"funder_award_id":"GM051387","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169467883.pdf","grobid_xml":"https://content.openalex.org/works/W2169467883.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2014025164","https://openalex.org/W2018310892","https://openalex.org/W2023115652","https://openalex.org/W2026465178","https://openalex.org/W2030367381","https://openalex.org/W2036026808","https://openalex.org/W2060971202","https://openalex.org/W2092233154","https://openalex.org/W2130706354","https://openalex.org/W2169346900"],"related_works":["https://openalex.org/W1657880117","https://openalex.org/W2595172197","https://openalex.org/W2127970246","https://openalex.org/W2084856301","https://openalex.org/W1001352512","https://openalex.org/W4382618745","https://openalex.org/W2885125400","https://openalex.org/W1989889224","https://openalex.org/W1987128138","https://openalex.org/W2372764048"],"abstract_inverted_index":{"vwysocki@email.arizona.edu.":[0]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
