{"id":"https://openalex.org/W4399032435","doi":"https://doi.org/10.1093/bioinformatics/btae335","title":"MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data","display_name":"MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data","publication_year":2024,"publication_date":"2024-05-24","ids":{"openalex":"https://openalex.org/W4399032435","doi":"https://doi.org/10.1093/bioinformatics/btae335","pmid":"https://pubmed.ncbi.nlm.nih.gov/38796681"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae335","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae335/57909407/btae335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae335/57909407/btae335.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014423704","display_name":"Marjan Faizi","orcid":"https://orcid.org/0000-0002-7170-7762"},"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"]},{"id":"https://openalex.org/I4210115614","display_name":"Boston VA Research Institute","ror":"https://ror.org/02419mc73","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marjan Faizi","raw_affiliation_strings":["Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States"],"raw_orcid":"https://orcid.org/0000-0002-7170-7762","affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210115614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038360314","display_name":"Ryan T. Fellers","orcid":"https://orcid.org/0000-0002-0710-3462"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan T Fellers","raw_affiliation_strings":["National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, IL 60208, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, IL 60208, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041166489","display_name":"Dan L\u00fc","orcid":"https://orcid.org/0000-0002-6952-9194"},"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"]},{"id":"https://openalex.org/I4210115614","display_name":"Boston VA Research Institute","ror":"https://ror.org/02419mc73","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan Lu","raw_affiliation_strings":["Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210115614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058369171","display_name":"Bryon Drown","orcid":"https://orcid.org/0000-0002-5631-512X"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bryon S Drown","raw_affiliation_strings":["National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, IL 60208, United States"],"raw_orcid":"https://orcid.org/0000-0002-5631-512X","affiliations":[{"raw_affiliation_string":"National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, IL 60208, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067072554","display_name":"Ashwini Jambhekar","orcid":"https://orcid.org/0000-0003-1078-6601"},"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"]},{"id":"https://openalex.org/I4210115614","display_name":"Boston VA Research Institute","ror":"https://ror.org/02419mc73","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashwini Jambhekar","raw_affiliation_strings":["Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210115614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058822360","display_name":"Galit Lahav","orcid":"https://orcid.org/0000-0003-4758-6427"},"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"]},{"id":"https://openalex.org/I4210115614","display_name":"Boston VA Research Institute","ror":"https://ror.org/02419mc73","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Galit Lahav","raw_affiliation_strings":["Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210115614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076257201","display_name":"Neil L. Kelleher","orcid":"https://orcid.org/0000-0002-8815-3372"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neil L Kelleher","raw_affiliation_strings":["National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, IL 60208, United States"],"raw_orcid":"https://orcid.org/0000-0002-8815-3372","affiliations":[{"raw_affiliation_string":"National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, IL 60208, United States","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056777354","display_name":"Jeremy Gunawardena","orcid":"https://orcid.org/0000-0002-7280-1152"},"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"]},{"id":"https://openalex.org/I4210115614","display_name":"Boston VA Research Institute","ror":"https://ror.org/02419mc73","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeremy Gunawardena","raw_affiliation_strings":["Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States"],"raw_orcid":"https://orcid.org/0000-0002-7280-1152","affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Blavatnik Institute at Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210115614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5056777354"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210115614"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5143,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54439643,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"40","issue":"6","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":0.6299999952316284,"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":0.6299999952316284,"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":0.34119999408721924,"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":0.00559999980032444,"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/mass-spectrometry","display_name":"Mass spectrometry","score":0.7232758402824402},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.451595276594162},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4316518306732178},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40350648760795593},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.24947884678840637}],"concepts":[{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.7232758402824402},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.451595276594162},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4316518306732178},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40350648760795593},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.24947884678840637},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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":"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"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":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae335","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae335/57909407/btae335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38796681","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38796681","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:pubmedcentral.nih.gov:11157153","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11157153","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11157153/pdf/btae335.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae335","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae335/57909407/btae335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1458171019","display_name":"Ein mathematisches Modell zur Interpretation des molekularen Codes des Tumorsuppressors p53","funder_award_id":"445690853","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1875415509","display_name":null,"funder_award_id":"P41 GM108569","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2926971636","display_name":null,"funder_award_id":"R35GM139572","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4801164401","display_name":null,"funder_award_id":"GM108569","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6424843072","display_name":null,"funder_award_id":"P41 GM108569","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7920464986","display_name":null,"funder_award_id":"P30 DA018310","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G8256491371","display_name":null,"funder_award_id":"P30 DA018310","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8799143874","display_name":null,"funder_award_id":"F32 CA246894","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G892048997","display_name":null,"funder_award_id":"P41 GM108569","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399032435.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1519955500","https://openalex.org/W1995454576","https://openalex.org/W2107003257","https://openalex.org/W2146482199","https://openalex.org/W2175428996","https://openalex.org/W2317393480","https://openalex.org/W2462197865","https://openalex.org/W2544360569","https://openalex.org/W2607310450","https://openalex.org/W2765786976","https://openalex.org/W2786505886","https://openalex.org/W2809710814","https://openalex.org/W2920207301","https://openalex.org/W2943223113","https://openalex.org/W2961184804","https://openalex.org/W3005216464","https://openalex.org/W3007615379","https://openalex.org/W3191137525","https://openalex.org/W4226056251","https://openalex.org/W4226062690","https://openalex.org/W6798345994"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"MOTIVATION:":[0],"Post-translational":[1],"modifications":[2],"(PTMs)":[3],"on":[4,37,57,173],"proteins":[5],"regulate":[6],"protein":[7,13,60,93,131,157,185],"structures":[8],"and":[9,95,151,160,177],"functions.":[10,49],"A":[11],"single":[12,106],"molecule":[14,94],"can":[15,21,43],"possess":[16],"multiple":[17,55],"modification":[18],"sites":[19,86],"that":[20,38,116,135,189],"accommodate":[22],"various":[23],"PTM":[24,41,118,164,199,209],"types,":[25],"leading":[26],"to":[27,46,68,73,87,90,104,143],"a":[28,70,105,111,156,192,197,213],"variety":[29],"of":[30,35,54,77,98,158,208,216],"different":[31,203],"patterns,":[32],"or":[33],"combinations":[34],"PTMs,":[36],"protein.":[39,107],"Different":[40],"patterns":[42,119,165,210],"give":[44],"rise":[45],"distinct":[47],"biological":[48],"To":[50],"facilitate":[51],"the":[52,58,75,91,141,182],"study":[53],"PTMs":[56,83,101],"same":[59,92],"molecule,":[61],"top-down":[62],"mass":[63,76,123,132,138,153],"spectrometry":[64,124,133],"(MS)":[65],"has":[66],"proven":[67],"be":[69,88],"useful":[71,193],"tool":[72,194],"measure":[74],"intact":[78,130],"proteins,":[79],"thereby":[80],"enabling":[81],"even":[82],"at":[84,228],"distant":[85],"assigned":[89],"allowing":[96],"determination":[97],"how":[99],"many":[100],"are":[102],"attached":[103],"RESULTS:":[108],"We":[109,187],"developed":[110],"Python":[112],"module":[113],"called":[114],"MSModDetector":[115,190],"studies":[117],"from":[120],"individual":[121],"ion":[122],"(I2MS)":[125],"data.":[126],"I2MS":[127,175,179],"is":[128,171,191,226],"an":[129],"approach":[134],"generates":[136],"true":[137],"spectra":[139],"without":[140],"need":[142],"infer":[144],"charge":[145],"states.":[146],"The":[147,169,223],"algorithm":[148,170],"first":[149],"detects":[150],"quantifies":[152],"shifts":[154],"for":[155,181,195],"interest":[159],"subsequently":[161],"infers":[162],"potential":[163],"using":[166],"linear":[167],"programming.":[168],"evaluated":[172],"simulated":[174],"data":[176,180],"experimental":[178],"tumor":[183],"suppressor":[184],"p53.":[186],"show":[188],"comparing":[196],"protein's":[198],"pattern":[200],"landscape":[201],"across":[202],"conditions.":[204],"An":[205],"improved":[206],"analysis":[207],"will":[211],"enable":[212],"deeper":[214],"understanding":[215],"PTM-regulated":[217],"cellular":[218],"processes.":[219],"AVAILABILITY":[220],"AND":[221],"IMPLEMENTATION:":[222],"source":[224],"code":[225],"available":[227],"https://github.com/marjanfaizi/MSModDetector.":[229]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
