{"id":"https://openalex.org/W4317556129","doi":"https://doi.org/10.1371/journal.pcbi.1010457","title":"Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics","display_name":"Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics","publication_year":2023,"publication_date":"2023-01-20","ids":{"openalex":"https://openalex.org/W4317556129","doi":"https://doi.org/10.1371/journal.pcbi.1010457","pmid":"https://pubmed.ncbi.nlm.nih.gov/36668672"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010457","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010457","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010457&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010457&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051713762","display_name":"Carlos Gueto-Tettay","orcid":"https://orcid.org/0000-0002-8496-6341"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Carlos Gueto-Tettay","raw_affiliation_strings":["Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-8496-6341","affiliations":[{"raw_affiliation_string":"Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052535909","display_name":"Di Tang","orcid":"https://orcid.org/0000-0001-6323-9375"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Di Tang","raw_affiliation_strings":["Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden"],"raw_orcid":"https://orcid.org/0000-0001-6323-9375","affiliations":[{"raw_affiliation_string":"Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090357790","display_name":"Lotta Happonen","orcid":"https://orcid.org/0000-0002-5922-4549"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Lotta Happonen","raw_affiliation_strings":["Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014096749","display_name":"Moritz Heusel","orcid":"https://orcid.org/0000-0002-8506-530X"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Moritz Heusel","raw_affiliation_strings":["Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-8506-530X","affiliations":[{"raw_affiliation_string":"Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082401528","display_name":"Hamed Khakzad","orcid":"https://orcid.org/0000-0002-8556-0650"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hamed Khakzad","raw_affiliation_strings":["Universit\u00e9 de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France"],"raw_orcid":"https://orcid.org/0000-0002-8556-0650","affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210121838","https://openalex.org/I90183372"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036451897","display_name":"Johan Malmstr\u00f6m","orcid":"https://orcid.org/0000-0002-2889-7169"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Johan Malmstr\u00f6m","raw_affiliation_strings":["Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089221737","display_name":"Lars Malmstr\u00f6m","orcid":"https://orcid.org/0000-0001-9885-9312"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Lars Malmstr\u00f6m","raw_affiliation_strings":["Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden"],"raw_orcid":"https://orcid.org/0000-0001-9885-9312","affiliations":[{"raw_affiliation_string":"Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089221737"],"corresponding_institution_ids":["https://openalex.org/I187531555"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2408,"currency":"EUR","value_usd":2597},"fwci":1.0731,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.70960372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"1","first_page":"e1010457","last_page":"e1010457"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9962000250816345,"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/computational-biology","display_name":"Computational biology","score":0.6760612726211548},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.6402113437652588},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5991129875183105},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.52442467212677},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.4576323330402374},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4356520175933838},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4283788800239563},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.4269601106643677},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42010068893432617},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2882111370563507},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.26761728525161743},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.18732613325119019},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1521303653717041},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.14633259177207947}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6760612726211548},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.6402113437652588},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5991129875183105},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.52442467212677},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.4576323330402374},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4356520175933838},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4283788800239563},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.4269601106643677},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42010068893432617},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2882111370563507},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26761728525161743},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.18732613325119019},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1521303653717041},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.14633259177207947}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":null,"qualifier_name":null,"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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D020539","descriptor_name":"Sequence Analysis, Protein","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":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1010457","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010457","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010457&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36668672","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36668672","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:HAL:hal-04403345v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04403345","pdf_url":"https://hal.science/hal-04403345/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 2023, 19 (1), pp.e1010457. ⟨10.1371/journal.pcbi.1010457⟩","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9891523","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9891523","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9891523/pdf/pcbi.1010457.pdf","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:bff3bbae203c4c88bfe6f05962fd52bc","is_oa":true,"landing_page_url":"https://doaj.org/article/bff3bbae203c4c88bfe6f05962fd52bc","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 1, p e1010457 (2023)","raw_type":"article"},{"id":"pmh:oai:infoscience.epfl.ch:302018","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/197054","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"WoS","raw_type":"research article"},{"id":"pmh:oai:lup.lub.lu.se:4c4d0359-e5be-4657-8c26-f47af388e476","is_oa":false,"landing_page_url":"https://lup.lub.lu.se/record/4c4d0359-e5be-4657-8c26-f47af388e476","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1553-734X","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010457","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010457","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010457&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4017602670","display_name":null,"funder_award_id":"2016.0023","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G8659301940","display_name":"Computational antibody och peptide design to fight antimicrobial resistance","funder_award_id":"2020-02419","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320323282","display_name":"Alfred \u00d6sterlunds Stiftelse","ror":"https://ror.org/020hnjs91"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4317556129.pdf","grobid_xml":"https://content.openalex.org/works/W4317556129.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W974578078","https://openalex.org/W1675027666","https://openalex.org/W1966824132","https://openalex.org/W1971887998","https://openalex.org/W1972244565","https://openalex.org/W1975450451","https://openalex.org/W1988536671","https://openalex.org/W1995638700","https://openalex.org/W1995693931","https://openalex.org/W2003261719","https://openalex.org/W2019513372","https://openalex.org/W2028673251","https://openalex.org/W2037883836","https://openalex.org/W2038615001","https://openalex.org/W2047275456","https://openalex.org/W2082392199","https://openalex.org/W2087934409","https://openalex.org/W2089273345","https://openalex.org/W2100518445","https://openalex.org/W2108223798","https://openalex.org/W2110417468","https://openalex.org/W2117713095","https://openalex.org/W2132629607","https://openalex.org/W2139397135","https://openalex.org/W2141036148","https://openalex.org/W2208034660","https://openalex.org/W2228775485","https://openalex.org/W2343251287","https://openalex.org/W2510167837","https://openalex.org/W2519691041","https://openalex.org/W2534641525","https://openalex.org/W2569631744","https://openalex.org/W2586066654","https://openalex.org/W2603081759","https://openalex.org/W2736859409","https://openalex.org/W2769374151","https://openalex.org/W2779450287","https://openalex.org/W2908908773","https://openalex.org/W2911188069","https://openalex.org/W2911925130","https://openalex.org/W2912581782","https://openalex.org/W2919115771","https://openalex.org/W2937143321","https://openalex.org/W2943223113","https://openalex.org/W2944245644","https://openalex.org/W2945219369","https://openalex.org/W2950954328","https://openalex.org/W2953112785","https://openalex.org/W2956118338","https://openalex.org/W2989698750","https://openalex.org/W3008586858","https://openalex.org/W3009182715","https://openalex.org/W3087184316","https://openalex.org/W3087556939","https://openalex.org/W3090166847","https://openalex.org/W3090341163","https://openalex.org/W3119966649","https://openalex.org/W3120631099","https://openalex.org/W3121301762","https://openalex.org/W3122450169","https://openalex.org/W3140854437","https://openalex.org/W3148275375","https://openalex.org/W3170277324","https://openalex.org/W3177828909","https://openalex.org/W3194955130","https://openalex.org/W3199380565","https://openalex.org/W3203934297","https://openalex.org/W4200249143","https://openalex.org/W4200492655","https://openalex.org/W4205417207","https://openalex.org/W4281790889","https://openalex.org/W4385245566","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W1488408180","https://openalex.org/W4375867731","https://openalex.org/W2360290178","https://openalex.org/W2035260723","https://openalex.org/W3005464483","https://openalex.org/W415785311","https://openalex.org/W2611989081","https://openalex.org/W3145527116","https://openalex.org/W2350543355","https://openalex.org/W3143512440"],"abstract_inverted_index":{"Generating":[0],"and":[1,25,83,133,190,204],"analyzing":[2,243],"overlapping":[3],"peptides":[4,101,136,152,206],"through":[5],"multienzymatic":[6,155],"digestion":[7,106,156],"is":[8],"an":[9],"efficient":[10],"procedure":[11],"for":[12,71,218],"de":[13,27,49,185,233],"novo":[14,28,50,186,234],"protein":[15,51],"using":[16,95],"from":[17,103,109,127,153],"bottom-up":[18],"mass":[19],"spectrometry":[20],"(MS).":[21],"Despite":[22],"improved":[23],"instrumentation":[24],"software,":[26],"MS":[29,62],"data":[30],"analysis":[31,235],"remains":[32],"challenging.":[33],"In":[34,64],"recent":[35],"years,":[36],"deep":[37,75,123,179],"learning":[38,76,124,180],"models":[39,56,77,125,182],"have":[40],"represented":[41],"a":[42,128,166,214],"performance":[43],"breakthrough.":[44],"Incorporating":[45],"that":[46,121,227],"technology":[47],"into":[48],"sequencing":[52,187],"workflows":[53],"require":[54],"machine-learning":[55],"capable":[57],"of":[58,85,100,107,130,160,176,194,220,245],"handling":[59],"highly":[60,131],"diverse":[61,135],"data.":[63],"this":[65],"study,":[66],"we":[67,172],"analyzed":[68],"the":[69,81,86,91,104,117,122,141,146,154,174,188,221,228,251],"requirements":[70],"assembling":[72],"such":[73,241],"generalizable":[74],"by":[78,150,183],"systemcally":[79],"varying":[80],"composition":[82],"size":[84,149],"training":[87,147],"set.":[88],"We":[89,225],"assessed":[90],"generated":[92,126],"models'":[93],"performances":[94],"two":[96],"test":[97,118],"sets":[98,119],"composed":[99],"originating":[102],"multienzyme":[105,178],"samples":[108,163,244],"various":[110],"species.":[111],"The":[112],"peptide":[113],"recall":[114],"values":[115],"on":[116],"showed":[120],"collection":[129],"N-":[132],"C-termini":[134],"generalized":[137],"76%":[138],"more":[139],"over":[140,201],"termini-restricted":[142],"ones.":[143],"Moreover,":[144],"expanding":[145],"set's":[148],"adding":[151],"with":[157],"five":[158,195],"proteases":[159,210],"several":[161,239],"species":[162],"led":[164],"to":[165,232],"2-3":[167],"fold":[168],"generalizability":[169],"gain.":[170],"Furthermore,":[171],"tested":[173],"applicability":[175],"these":[177],"(MEM)":[181],"fully":[184],"heavy":[189],"light":[191],"monomeric":[192],"chains":[193],"commercial":[196],"antibodies":[197],"(mAbs).":[198],"MEMs":[199],"extracted":[200],"10000":[202],"matching":[203],"overlapped":[205],"across":[207],"six":[208],"different":[209],"mAb":[211],"samples,":[212],"achieving":[213],"100%":[215],"sequence":[216],"coverage":[217],"8":[219],"ten":[222],"polypeptide":[223],"chains.":[224],"foretell":[226],"MEMs'":[229],"proven":[230],"improvements":[231],"will":[236],"positively":[237],"impact":[238],"applications,":[240],"as":[242],"high":[246],"complexity,":[247],"unknown":[248],"nature,":[249],"or":[250],"peptidomics":[252],"field.":[253]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}