{"id":"https://openalex.org/W2167797060","doi":"https://doi.org/10.1186/1471-2105-8-s7-s24","title":"ProtQuant: a tool for the label-free quantification of MudPIT proteomics data","display_name":"ProtQuant: a tool for the label-free quantification of MudPIT proteomics data","publication_year":2007,"publication_date":"2007-11-01","ids":{"openalex":"https://openalex.org/W2167797060","doi":"https://doi.org/10.1186/1471-2105-8-s7-s24","mag":"2167797060","pmid":"https://pubmed.ncbi.nlm.nih.gov/18047724"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-s7-s24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-s7-s24","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-S7-S24","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-S7-S24","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112009477","display_name":"Susan M. Bridges","orcid":null},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Susan M Bridges","raw_affiliation_strings":["Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA. bridges@cse.msstate.edu","Institute for Digital Biology, Mississippi State University, Starkville, USA","Department of Computer Science and Engineering, Mississippi State University, Starkville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA. bridges@cse.msstate.edu","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069352006","display_name":"G Bryce Magee","orcid":null},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G Bryce Magee","raw_affiliation_strings":["Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","Department of Computer Science and Engineering, Mississippi State University, Starkville, USA","Institute for Digital Biology, Mississippi State University, Starkville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100332800","display_name":"Nan Wang","orcid":"https://orcid.org/0000-0003-4630-5216"},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nan Wang","raw_affiliation_strings":["Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, USA","Department of Computer Science and Engineering, Mississippi State University, Starkville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033655450","display_name":"W. Paul Williams","orcid":"https://orcid.org/0000-0002-7827-3186"},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W Paul Williams","raw_affiliation_strings":["Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, USA","USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State University, Starkville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060219125","display_name":"Shane C. Burgess","orcid":"https://orcid.org/0000-0003-0076-9461"},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shane C Burgess","raw_affiliation_strings":["College of Veterinary Medicine, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","Mississippi Agriculture and Forestry Experiment Station, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, USA","Mississippi Agriculture and Forestry Experiment Station, Mississippi State University, Starkville, USA","College of Veterinary Medicine, Mississippi State University, Starkville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Mississippi Agriculture and Forestry Experiment Station, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Mississippi Agriculture and Forestry Experiment Station, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"College of Veterinary Medicine, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114125460","display_name":"Bindu Nanduri","orcid":null},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bindu Nanduri","raw_affiliation_strings":["College of Veterinary Medicine, Mississippi State University, Starkville, MS, 39762, USA","Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","College of Veterinary Medicine, Mississippi State University, Starkville, USA","Institute for Digital Biology, Mississippi State University, Starkville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, MS, 39762, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"College of Veterinary Medicine, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Institute for Digital Biology, Mississippi State University, Starkville, USA","institution_ids":["https://openalex.org/I99041443"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5112009477"],"corresponding_institution_ids":["https://openalex.org/I99041443"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.3944,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.96399849,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"S7","first_page":"S24","last_page":"S24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9934999942779541,"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":0.9934999942779541,"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/T13127","display_name":"Biotin and Related Studies","score":0.00279999990016222,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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"}},{"id":"https://openalex.org/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.000699999975040555,"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/label-free-quantification","display_name":"Label-free quantification","score":0.7637467980384827},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6889116764068604},{"id":"https://openalex.org/keywords/quantitative-proteomics","display_name":"Quantitative proteomics","score":0.5743423104286194},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5210213661193848},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.49166756868362427},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.46487879753112793},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.45284852385520935},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.4476182758808136},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.4249950051307678},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4019988775253296},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32532376050949097},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.18395063281059265},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17873013019561768},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09948745369911194}],"concepts":[{"id":"https://openalex.org/C73090800","wikidata":"https://www.wikidata.org/wiki/Q6466869","display_name":"Label-free quantification","level":5,"score":0.7637467980384827},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6889116764068604},{"id":"https://openalex.org/C80311884","wikidata":"https://www.wikidata.org/wiki/Q7268939","display_name":"Quantitative proteomics","level":4,"score":0.5743423104286194},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5210213661193848},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.49166756868362427},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.46487879753112793},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.45284852385520935},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.4476182758808136},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4249950051307678},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4019988775253296},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32532376050949097},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18395063281059265},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17873013019561768},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09948745369911194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","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":"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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-s7-s24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-s7-s24","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-S7-S24","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18047724","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18047724","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:7579a81482c7431b8d68b7739ec2cf6a","is_oa":false,"landing_page_url":"https://doaj.org/article/7579a81482c7431b8d68b7739ec2cf6a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss Suppl 7, p S24 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2099493","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2099493","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-s7-s24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-s7-s24","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-S7-S24","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6334716638","display_name":"Innovations through Computational Sciences","funder_award_id":"0556308","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7251575830","display_name":null,"funder_award_id":"EPS-0556308-06040293","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332694","display_name":"Bagley College of Engineering, Mississippi State University","ror":"https://ror.org/0432jq872"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167797060.pdf","grobid_xml":"https://content.openalex.org/works/W2167797060.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1597678601","https://openalex.org/W1975558168","https://openalex.org/W1981593008","https://openalex.org/W1997504014","https://openalex.org/W2026465178","https://openalex.org/W2047275456","https://openalex.org/W2052365477","https://openalex.org/W2059315009","https://openalex.org/W2065617511","https://openalex.org/W2095732971","https://openalex.org/W2096057003","https://openalex.org/W2105869274","https://openalex.org/W2106801905","https://openalex.org/W2111062197","https://openalex.org/W2111208057","https://openalex.org/W2112078820","https://openalex.org/W2120016245","https://openalex.org/W2123886946","https://openalex.org/W2148490163","https://openalex.org/W2156022009"],"related_works":["https://openalex.org/W2944683884","https://openalex.org/W2160416873","https://openalex.org/W3081950544","https://openalex.org/W3089696757","https://openalex.org/W2000259163","https://openalex.org/W2014032285","https://openalex.org/W2374027747","https://openalex.org/W1990519872","https://openalex.org/W4376133284","https://openalex.org/W1574322319"],"abstract_inverted_index":{"BACKGROUND:":[0],"Effective":[1],"and":[2,24,64,79,92,144,161,200,207,288,299,308],"economical":[3],"methods":[4,48,70,105],"for":[5,106,131,142,149,157,163,172,219,224,228,245,274,278,305,318],"quantitative":[6],"analysis":[7],"of":[8,20,47,94,103,159,196,205,210,261,264,293],"high":[9],"throughput":[10],"mass":[11],"spectrometry":[12],"data":[13,247,306],"are":[14,49,71,116],"essential":[15],"to":[16,51,240,267],"meet":[17],"the":[18,65,74,113,137,164,169,194,197,301,319],"goals":[19],"directly":[21],"identifying,":[22],"characterizing,":[23],"quantifying":[25],"proteins":[26],"from":[27,177],"a":[28,38,101,128,182,216,272,315],"particular":[29],"cell":[30],"state.":[31],"Multidimensional":[32],"Protein":[33],"Identification":[34],"Technology":[35],"(MudPIT)":[36],"is":[37,190,271,312],"common":[39],"approach":[40],"used":[41,50,227,322],"in":[42,56,112,257],"protein":[43,54,77,107,133,175,275,294],"identification.":[44],"Two":[45],"types":[46],"detect":[52],"differential":[53,262],"expression":[55,263],"MudPIT":[57,178],"experiments:":[58],"those":[59],"involving":[60],"stable":[61],"isotope":[62],"labelling":[63],"so-called":[66],"label-free":[67,104,132,291],"methods.":[68,124],"Label-free":[69],"based":[72],"on":[73],"relationship":[75],"between":[76],"abundance":[78],"sampling":[80],"statistics":[81],"such":[82],"as":[83,314],"peptide":[84,89,95,225,238],"count,":[85,87],"spectral":[86],"probabilistic":[88],"identification":[90],"scores,":[91],"sum":[93],"Sequest":[96,298],"XCorr":[97],"scores":[98,226,239],"(SigmaXCorr).":[99],"Although":[100],"number":[102,204,209],"quantification":[108,134,143,176,276,292],"have":[109],"been":[110],"described":[111],"literature,":[114],"there":[115],"few":[117],"publicly":[118],"available":[119,313],"tools":[120],"that":[121,135,251],"implement":[122],"these":[123],"We":[125,249],"describe":[126],"ProtQuant,":[127],"Java-based":[129],"tool":[130,273],"uses":[136,235],"previously":[138],"published":[139],"SigmaXCorr":[140,170],"method":[141,148,171,218],"includes":[145],"an":[146,254,282],"improved":[147],"handling":[150],"missing":[151,222,246],"data.":[152],"RESULTS:":[153],"ProtQuant":[154,180,214,270,286,311],"was":[155],"designed":[156],"ease":[158],"use":[160,280],"portability":[162],"bench":[165,325],"scientist.":[166],"It":[167],"implements":[168,215],"label":[173],"free":[174],"datasets.":[179],"has":[181],"graphical":[183],"user":[184,284,302],"interface,":[185],"accepts":[186],"multiple":[187],"file":[188],"formats,":[189],"not":[191],"limited":[192],"by":[193,323],"size":[195],"input":[198],"files,":[199],"can":[201],"process":[202],"any":[203,208],"replicates":[206],"treatments.":[211],"In":[212],"addition,":[213],"new":[217,231],"dealing":[220],"with":[221,281,297,303],"values":[223,244],"quantification.":[229],"The":[230],"algorithm,":[232],"called":[233],"SigmaXCorr*,":[234],"\"below":[236],"threshold\"":[237],"provide":[241],"meaningful":[242],"non-zero":[243],"points.":[248],"demonstrate":[250],"SigmaXCorr*":[252],"produces":[253],"average":[255],"reduction":[256],"false":[258],"positive":[259],"identifications":[260],"25%":[265],"compared":[266],"SigmaXCorr.":[268],"CONCLUSION:":[269],"built":[277],"multi-platform":[279],"intuitive":[283],"interface.":[285],"efficiently":[287],"uniquely":[289],"performs":[290],"datasets":[295],"produced":[296],"provides":[300],"facilities":[304],"management":[307],"analysis.":[309],"Importantly,":[310],"self-installing":[316],"executable":[317],"Windows":[320],"environment":[321],"many":[324],"scientists.":[326]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
