{"id":"https://openalex.org/W2125419939","doi":"https://doi.org/10.1093/bioinformatics/btp362","title":"A statistical framework for protein quantitation in bottom-up MS-based proteomics","display_name":"A statistical framework for protein quantitation in bottom-up MS-based proteomics","publication_year":2009,"publication_date":"2009-06-17","ids":{"openalex":"https://openalex.org/W2125419939","doi":"https://doi.org/10.1093/bioinformatics/btp362","mag":"2125419939","pmid":"https://pubmed.ncbi.nlm.nih.gov/19535538"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp362","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2028/48993906/bioinformatics_25_16_2028.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/25/16/2028/48993906/bioinformatics_25_16_2028.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013624035","display_name":"Yuliya V. Karpievitch","orcid":"https://orcid.org/0000-0003-2586-3358"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuliya Karpievitch","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058997368","display_name":"Jeffrey A. Stanley","orcid":"https://orcid.org/0000-0003-2355-480X"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff Stanley","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069163518","display_name":"Thomas Taverner","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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Taverner","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101462938","display_name":"Jianhua Z. Huang","orcid":"https://orcid.org/0000-0002-7735-3002"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianhua Huang","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua N. Adkins","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068615364","display_name":"Charles Ansong","orcid":"https://orcid.org/0000-0001-5793-8559"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles Ansong","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091655566","display_name":"Fred Heffron","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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fred Heffron","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034592694","display_name":"Thomas Metz","orcid":"https://orcid.org/0000-0001-6049-3968"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas O. Metz","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075235007","display_name":"Weijun Qian","orcid":"https://orcid.org/0000-0002-5393-2827"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei-Jun Qian","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049559685","display_name":"Hyunjin Yoon","orcid":"https://orcid.org/0000-0002-2252-9402"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyunjin Yoon","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"middle","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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard D. Smith","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019742058","display_name":"Alan R. Dabney","orcid":"https://orcid.org/0000-0002-1240-4171"},"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"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan R. Dabney","raw_affiliation_strings":["1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, 2Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352 and 3Molecular Microbiology and Immunology, Oregon Health and Science University, Mail Code L220, Portland, OR 97201, USA","institution_ids":["https://openalex.org/I142606810","https://openalex.org/I165690674","https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.3398,"has_fulltext":true,"cited_by_count":181,"citation_normalized_percentile":{"value":0.97469344,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"25","issue":"16","first_page":"2028","last_page":"2034"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9922999739646912,"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":0.9922999739646912,"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":0.003800000064074993,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.0006000000284984708,"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/proteomics","display_name":"Proteomics","score":0.6872248649597168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5441743731498718},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5324419736862183},{"id":"https://openalex.org/keywords/quantitative-proteomics","display_name":"Quantitative proteomics","score":0.4981496334075928},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.35592442750930786},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32307904958724976},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21469253301620483},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16071867942810059}],"concepts":[{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6872248649597168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5441743731498718},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5324419736862183},{"id":"https://openalex.org/C80311884","wikidata":"https://www.wikidata.org/wiki/Q7268939","display_name":"Quantitative proteomics","level":4,"score":0.4981496334075928},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.35592442750930786},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32307904958724976},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21469253301620483},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16071867942810059},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btp362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp362","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2028/48993906/bioinformatics_25_16_2028.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:19535538","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19535538","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:ecite.utas.edu.au:80883","is_oa":false,"landing_page_url":"http://ecite.utas.edu.au/80883","pdf_url":null,"source":{"id":"https://openalex.org/S4306401569","display_name":"eCite Digital Repository (University of Tasmania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I129801699","host_organization_name":"University of Tasmania","host_organization_lineage":["https://openalex.org/I129801699"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Refereed Article"},{"id":"pmh:oai:europepmc.org:2007490","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2723007","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"},{"id":"pmh:oai:figshare.com:article/22894712","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/A_statistical_framework_for_protein_quantitation_in_bottom-up_MS-based_proteomics/22894712","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp362","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2028/48993906/bioinformatics_25_16_2028.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":[],"awards":[{"id":"https://openalex.org/G5376322187","display_name":null,"funder_award_id":"DK070146","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320338354","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125419939.pdf","grobid_xml":"https://content.openalex.org/works/W2125419939.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1597883912","https://openalex.org/W1943548283","https://openalex.org/W1964895626","https://openalex.org/W1972556338","https://openalex.org/W1989711406","https://openalex.org/W1996644428","https://openalex.org/W2006305154","https://openalex.org/W2017199538","https://openalex.org/W2023096047","https://openalex.org/W2027469236","https://openalex.org/W2044758663","https://openalex.org/W2045638068","https://openalex.org/W2050783490","https://openalex.org/W2071030970","https://openalex.org/W2096863518","https://openalex.org/W2101938218","https://openalex.org/W2105381419","https://openalex.org/W2110065044","https://openalex.org/W2111208057","https://openalex.org/W2112078820","https://openalex.org/W2122759946","https://openalex.org/W2147830145","https://openalex.org/W2152180036","https://openalex.org/W2160110467","https://openalex.org/W2164343224","https://openalex.org/W2480680997","https://openalex.org/W2797043077","https://openalex.org/W4213201159","https://openalex.org/W4229628595","https://openalex.org/W6649376304"],"related_works":["https://openalex.org/W2160416873","https://openalex.org/W3081950544","https://openalex.org/W3089696757","https://openalex.org/W2000259163","https://openalex.org/W2374027747","https://openalex.org/W1990519872","https://openalex.org/W3005464483","https://openalex.org/W1574322319","https://openalex.org/W2088324202","https://openalex.org/W2097713953"],"abstract_inverted_index":{"MOTIVATION:":[0],"Quantitative":[1],"mass":[2],"spectrometry-based":[3],"proteomics":[4,126],"requires":[5],"protein-level":[6,58],"estimates":[7],"and":[8,23,54,60,69,83],"associated":[9],"confidence":[10],"measures.":[11],"Challenges":[12],"include":[13],"the":[14,36,99,124],"presence":[15],"of":[16,81,89],"low":[17],"quality":[18],"or":[19],"incorrectly":[20],"identified":[21],"peptides":[22,84],"informative":[24,49],"missingness.":[25],"Furthermore,":[26],"models":[27],"are":[28,95,106],"required":[29],"for":[30,48,79],"rolling":[31],"peptide-level":[32],"information":[33],"up":[34],"to":[35,66,97,108],"protein":[37],"level.":[38],"RESULTS:":[39],"We":[40,73],"present":[41],"a":[42],"statistical":[43],"model":[44,63],"that":[45],"carefully":[46],"accounts":[47],"missingness":[50],"in":[51,123],"peak":[52],"intensities":[53],"allows":[55],"unbiased,":[56],"model-based,":[57,77],"estimation":[59],"inference.":[61],"The":[62,117],"is":[64],"applicable":[65],"both":[67],"label-based":[68],"label-free":[70],"quantitation":[71],"experiments.":[72],"also":[74],"provide":[75],"automated,":[76],"algorithms":[78],"filtering":[80],"proteins":[82],"as":[85,87],"well":[86],"imputation":[88],"missing":[90],"values.":[91],"Two":[92],"LC/MS":[93],"datasets":[94],"used":[96],"illustrate":[98],"methods.":[100],"In":[101],"simulation":[102],"studies,":[103],"our":[104],"methods":[105],"shown":[107],"achieve":[109],"substantially":[110],"more":[111],"discoveries":[112],"than":[113],"standard":[114],"alternatives.":[115],"AVAILABILITY:":[116],"software":[118],"has":[119],"been":[120],"made":[121],"available":[122],"open-source":[125],"platform":[127],"DAnTE":[128],"(http://omics.pnl.gov/software/).":[129]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":21},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":19}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
