{"id":"https://openalex.org/W2124114991","doi":"https://doi.org/10.1093/bioinformatics/btm281","title":"VIPER: an advanced software package to support high-throughput LC-MS peptide identification","display_name":"VIPER: an advanced software package to support high-throughput LC-MS peptide identification","publication_year":2007,"publication_date":"2007-06-01","ids":{"openalex":"https://openalex.org/W2124114991","doi":"https://doi.org/10.1093/bioinformatics/btm281","mag":"2124114991","pmid":"https://pubmed.ncbi.nlm.nih.gov/17545182"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm281","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm281","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/15/2021/49815207/bioinformatics_23_15_2021.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/23/15/2021/49815207/bioinformatics_23_15_2021.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005196385","display_name":"Matthew Monroe","orcid":"https://orcid.org/0000-0002-1210-7169"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew E. Monroe","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99354, USA","Pacific Northwest National Laboratory, Richland, WA, 99354, USA"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99354, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA, 99354, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052412732","display_name":"Nikola Toli\u0107","orcid":"https://orcid.org/0000-0003-3950-9130"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikola Toli\u0107","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99354, USA","Pacific Northwest National Laboratory, Richland, WA, 99354, USA"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99354, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA, 99354, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112445699","display_name":"Navdeep Jaitly","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Navdeep Jaitly","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99354, USA","Pacific Northwest National Laboratory, Richland, WA, 99354, USA"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99354, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA, 99354, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024658816","display_name":"Jason L. Shaw","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason L. Shaw","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99354, USA","Pacific Northwest National Laboratory, Richland, WA, 99354, USA"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99354, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA, 99354, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089245822","display_name":"Joshua Adkins","orcid":"https://orcid.org/0000-0003-0399-0700"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua N. Adkins","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99354, USA","Pacific Northwest National Laboratory, Richland, WA, 99354, USA"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99354, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA, 99354, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023982706","display_name":"Richard Smith","orcid":"https://orcid.org/0000-0002-2381-2349"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard D. Smith","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99354, USA","Pacific Northwest National Laboratory, Richland, WA, 99354, USA"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99354, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA, 99354, USA","institution_ids":["https://openalex.org/I142606810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005196385"],"corresponding_institution_ids":["https://openalex.org/I142606810"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":10.4093,"has_fulltext":false,"cited_by_count":184,"citation_normalized_percentile":{"value":0.99160532,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"23","issue":"15","first_page":"2021","last_page":"2023"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9994999766349792,"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":0.9983999729156494,"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/pipeline","display_name":"Pipeline (software)","score":0.7469131350517273},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7372745275497437},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.608085036277771},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.551956295967102},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5197538733482361},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4376010000705719},{"id":"https://openalex.org/keywords/viper","display_name":"VIPeR","score":0.42956608533859253},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09594717621803284},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09155440330505371},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07185599207878113},{"id":"https://openalex.org/keywords/venom","display_name":"Venom","score":0.06852021813392639}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7469131350517273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7372745275497437},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.608085036277771},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.551956295967102},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5197538733482361},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4376010000705719},{"id":"https://openalex.org/C2780389661","wikidata":"https://www.wikidata.org/wiki/Q1528875","display_name":"VIPeR","level":3,"score":0.42956608533859253},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09594717621803284},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09155440330505371},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07185599207878113},{"id":"https://openalex.org/C2779448229","wikidata":"https://www.wikidata.org/wiki/Q3386847","display_name":"Venom","level":2,"score":0.06852021813392639},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm281","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm281","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/15/2021/49815207/bioinformatics_23_15_2021.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:17545182","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17545182","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm281","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm281","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/15/2021/49815207/bioinformatics_23_15_2021.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":[{"display_name":"Industry, innovation and infrastructure","score":0.6299999952316284,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2124114991.pdf","grobid_xml":"https://content.openalex.org/works/W2124114991.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1519955500","https://openalex.org/W1578462894","https://openalex.org/W1597678601","https://openalex.org/W1981593008","https://openalex.org/W1991165514","https://openalex.org/W2026465178","https://openalex.org/W2053679126","https://openalex.org/W2073470877","https://openalex.org/W2101938218","https://openalex.org/W2130706354"],"related_works":["https://openalex.org/W15444843","https://openalex.org/W137568860","https://openalex.org/W2025448779","https://openalex.org/W4233990269","https://openalex.org/W2414993768","https://openalex.org/W2992074815","https://openalex.org/W3114349555","https://openalex.org/W2515902514","https://openalex.org/W2375218795","https://openalex.org/W2393010557"],"abstract_inverted_index":{"VIPER":[0],"may":[1],"be":[2],"downloaded":[3],"free":[4],"of":[5],"charge":[6],"at":[7],"http://ncrr.pnl.gov/software/":[8]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":20},{"year":2012,"cited_by_count":17}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
