{"id":"https://openalex.org/W4414322281","doi":"https://doi.org/10.1101/2025.09.10.675407","title":"Library-Free Multiplexed Targeted Proteomics Enables Quantitative Protein-Level Genotyping","display_name":"Library-Free Multiplexed Targeted Proteomics Enables Quantitative Protein-Level Genotyping","publication_year":2025,"publication_date":"2025-09-16","ids":{"openalex":"https://openalex.org/W4414322281","doi":"https://doi.org/10.1101/2025.09.10.675407","pmid":"https://pubmed.ncbi.nlm.nih.gov/41001004","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12458936"},"language":"en","primary_location":{"id":"doi:10.1101/2025.09.10.675407","doi":"https://doi.org/10.1101/2025.09.10.675407","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.10.675407","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/09/16/2025.09.10.675407.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/09/16/2025.09.10.675407.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016142394","display_name":"Steven R. Shuken","orcid":"https://orcid.org/0000-0002-2782-2165","observed_orcids":["https://orcid.org/0000-0002-2782-2165"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven R. Shuken","raw_affiliation_strings":["Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA","Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 025, USA"],"raw_orcid":"https://orcid.org/0000-0002-2782-2165","affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 025, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079793809","display_name":"Steven P. Gygi","orcid":"https://orcid.org/0000-0001-7626-0034","observed_orcids":["https://orcid.org/0000-0001-7626-0034"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven P. Gygi","raw_affiliation_strings":["Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA","Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 025, USA"],"raw_orcid":"https://orcid.org/0000-0001-7626-0034","affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 025, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5079793809"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9955999851226807,"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":0.9955999851226807,"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":0.003100000089034438,"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":0.0003000000142492354,"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/targeted-proteomics","display_name":"targeted proteomics","score":0.8700000047683716},{"id":"https://openalex.org/keywords/tandem-mass-tags","display_name":"tandem mass tags","score":0.6940000057220459},{"id":"https://openalex.org/keywords/kras-g13d","display_name":"KRAS G13D","score":0.9129999876022339},{"id":"https://openalex.org/keywords/cancer-cell-lines","display_name":"cancer cell lines","score":0.9509999752044678},{"id":"https://openalex.org/keywords/retention-time-prediction","display_name":"retention time prediction","score":0.675000011920929}],"concepts":[{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6588000059127808},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6521999835968018},{"id":"https://openalex.org/C80311884","wikidata":"https://www.wikidata.org/wiki/Q7268939","display_name":"Quantitative proteomics","level":4,"score":0.5038999915122986},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.4918999969959259},{"id":"https://openalex.org/C86153913","wikidata":"https://www.wikidata.org/wiki/Q7682439","display_name":"Tandem mass tag","level":5,"score":0.4620000123977661},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4523000121116638},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.43950000405311584},{"id":"https://openalex.org/C2781187634","wikidata":"https://www.wikidata.org/wiki/Q20969980","display_name":"KRAS","level":4,"score":0.426800012588501},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3637999892234802},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.36239999532699585},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3564999997615814},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.3497999906539917},{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.33149999380111694},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.3100999891757965},{"id":"https://openalex.org/C2994372470","wikidata":"https://www.wikidata.org/wiki/Q4118072","display_name":"Cancer cell lines","level":4,"score":0.29589998722076416},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C73090800","wikidata":"https://www.wikidata.org/wiki/Q6466869","display_name":"Label-free quantification","level":5,"score":0.27880001068115234},{"id":"https://openalex.org/C34905852","wikidata":"https://www.wikidata.org/wiki/Q3943646","display_name":"Stable isotope labeling by amino acids in cell culture","level":4,"score":0.2736000120639801},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.26669999957084656},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2574999928474426},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2563000023365021}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1101/2025.09.10.675407","doi":"https://doi.org/10.1101/2025.09.10.675407","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.10.675407","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/09/16/2025.09.10.675407.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41001004","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41001004","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12458936","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12458936/","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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:11267574","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12458936","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,"listed_in":[],"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2025.09.10.675407","doi":"https://doi.org/10.1101/2025.09.10.675407","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.10.675407","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/09/16/2025.09.10.675407.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G315888112","display_name":"New Sample Multiplexing Technologies to Identify Chemical Probes and Illuminate Ubiquitin Biology","funder_award_id":"R01GM067945","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000891665","display_name":"Validation and Kinetic Characterization of Blood-Cerebrospinal Fluid Barrier-Traversing Proteins in Aging With Library-Free Multiplexed Targeted Proteomics","funder_award_id":"K99AG088297","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414322281.pdf","grobid_xml":"https://content.openalex.org/works/W4414322281.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1990273811","https://openalex.org/W2073401456","https://openalex.org/W2089273345","https://openalex.org/W3048539016","https://openalex.org/W3203113379","https://openalex.org/W3208349679","https://openalex.org/W4223592008","https://openalex.org/W4241548761","https://openalex.org/W4280519594","https://openalex.org/W4318070663","https://openalex.org/W4319032825","https://openalex.org/W4361222545","https://openalex.org/W4378952025","https://openalex.org/W4389048382","https://openalex.org/W4394690681","https://openalex.org/W4402412259","https://openalex.org/W4403825747","https://openalex.org/W6927118510"],"related_works":["https://openalex.org/W4389048382","https://openalex.org/W4414225398","https://openalex.org/W4394690681","https://openalex.org/W4319032825","https://openalex.org/W7204180384","https://openalex.org/W4238357973","https://openalex.org/W4399274788","https://openalex.org/W2571000140","https://openalex.org/W4408392549","https://openalex.org/W2057715443"],"abstract_inverted_index":{"Existing":[0],"targeted":[1,40],"mass":[2,46,52],"spectrometry":[3],"methods":[4],"require":[5],"synthetic":[6],"standard":[7],"peptides,":[8],"manual":[9],"scan":[10],"scheduling,":[11],"or":[12],"data":[13,37],"libraries":[14],"to":[15,57],"quantify":[16],"target":[17,49],"proteins.":[18],"Here":[19],"we":[20],"present":[21],"GoDig-LiF,":[22],"which":[23],"uses":[24],"spectra":[25],"and":[26,51],"retention":[27],"times":[28],"predicted":[29],"by":[30],"the":[31,58],"Prosit-TMT":[32],"model":[33],"in":[34,63],"place":[35],"of":[36,60],"libraries,":[38],"enabling":[39],"proteomics":[41],"with":[42],"only":[43],"a":[44],"tandem":[45],"tag-labeled":[47],"sample,":[48],"list,":[50],"spectrometer.":[53],"We":[54],"applied":[55],"GoDig-LiF":[56],"quantification":[59],"mutated":[61],"proteins":[62],"cancer":[64],"cell":[65],"lines,":[66],"including":[67],"KRAS":[68],"G13D.":[69]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2025-10-10T00:00:00"}