{"id":"https://openalex.org/W2014201551","doi":"https://doi.org/10.1002/pmic.201400180","title":"A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites","display_name":"A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites","publication_year":2014,"publication_date":"2014-08-22","ids":{"openalex":"https://openalex.org/W2014201551","doi":"https://doi.org/10.1002/pmic.201400180","mag":"2014201551","pmid":"https://pubmed.ncbi.nlm.nih.gov/25156699","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4391000"},"language":"en","primary_location":{"id":"doi:10.1002/pmic.201400180","doi":"https://doi.org/10.1002/pmic.201400180","is_oa":true,"landing_page_url":"https://doi.org/10.1002/pmic.201400180","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.201400180","source":{"id":"https://openalex.org/S182655450","display_name":"PROTEOMICS","issn_l":"1615-9853","issn":["1615-9853","1615-9861"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PROTEOMICS","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.201400180","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003556658","display_name":"Alexander Koch","orcid":"https://orcid.org/0000-0002-9804-7602","observed_orcids":["https://orcid.org/0000-0002-9804-7602"]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Alexander Koch","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","These authors contributed equally to this work"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"These authors contributed equally to this work","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042462258","display_name":"Daria Fija\u0142kowska","orcid":"https://orcid.org/0000-0002-2084-146X","observed_orcids":["https://orcid.org/0000-0002-2084-146X"]},"institutions":[{"id":"https://openalex.org/I2802017950","display_name":"Vlaams Instituut voor Biotechnologie","ror":"https://ror.org/03xrhmk39","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Daria Gawron","raw_affiliation_strings":["Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium","These authors contributed equally to this work"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium","institution_ids":["https://openalex.org/I2802017950"]},{"raw_affiliation_string":"These authors contributed equally to this work","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048875611","display_name":"Sandra Steyaert","orcid":"https://orcid.org/0000-0002-0996-1364","observed_orcids":["https://orcid.org/0000-0002-0996-1364"]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Sandra Steyaert","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017488032","display_name":"Elvis Ndah","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2802017950","display_name":"Vlaams Instituut voor Biotechnologie","ror":"https://ror.org/03xrhmk39","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Elvis Ndah","raw_affiliation_strings":["Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium","Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium","institution_ids":["https://openalex.org/I2802017950"]},{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071163795","display_name":"Jeroen Crapp\u00e9","orcid":"https://orcid.org/0000-0003-1677-9533","observed_orcids":["https://orcid.org/0000-0003-1677-9533"]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Jeroen Crapp\u00e9","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088498339","display_name":"Sarah De Keulenaer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Sarah De Keulenaer","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024401362","display_name":"Ellen De Meester","orcid":"https://orcid.org/0009-0008-5376-9557","observed_orcids":["https://orcid.org/0009-0008-5376-9557"]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Ellen De Meester","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101707615","display_name":"Ming Ma","orcid":"https://orcid.org/0000-0001-7481-6705","observed_orcids":["https://orcid.org/0000-0001-7481-6705"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming Ma","raw_affiliation_strings":["Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087514362","display_name":"Ben Shen","orcid":"https://orcid.org/0000-0002-9750-5982","observed_orcids":["https://orcid.org/0000-0002-9750-5982"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Shen","raw_affiliation_strings":["Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072800163","display_name":"Kris Gevaert","orcid":"https://orcid.org/0000-0002-4237-0283","observed_orcids":["https://orcid.org/0000-0002-4237-0283"]},"institutions":[{"id":"https://openalex.org/I2802017950","display_name":"Vlaams Instituut voor Biotechnologie","ror":"https://ror.org/03xrhmk39","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Kris Gevaert","raw_affiliation_strings":["Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium","institution_ids":["https://openalex.org/I2802017950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024174357","display_name":"Wim Van Criekinge","orcid":"https://orcid.org/0000-0003-2971-5539","observed_orcids":["https://orcid.org/0000-0003-2971-5539"]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Wim Van Criekinge","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079964045","display_name":"Petra Van Damme","orcid":"https://orcid.org/0000-0001-9090-027X","observed_orcids":["https://orcid.org/0000-0001-9090-027X"]},"institutions":[{"id":"https://openalex.org/I2802017950","display_name":"Vlaams Instituut voor Biotechnologie","ror":"https://ror.org/03xrhmk39","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Petra Van Damme","raw_affiliation_strings":["Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium","institution_ids":["https://openalex.org/I2802017950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058473391","display_name":"Gerben Menschaert","orcid":"https://orcid.org/0000-0002-7575-2085","observed_orcids":["https://orcid.org/0000-0002-7575-2085"]},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Gerben Menschaert","raw_affiliation_strings":["Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5058473391","https://openalex.org/A5079964045"],"corresponding_institution_ids":["https://openalex.org/I2802017950","https://openalex.org/I32597200"],"apc_list":{"value":4650,"currency":"USD","value_usd":4650},"apc_paid":null,"fwci":4.2991,"has_fulltext":true,"cited_by_count":76,"citation_normalized_percentile":{"value":0.9609224,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"14","issue":"23-24","first_page":"2688","last_page":"2698"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9945999979972839,"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":0.9945999979972839,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0010000000474974513,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0007999999797903001,"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/proteogenomics","display_name":"proteogenomics","score":0.9900000095367432},{"id":"https://openalex.org/keywords/ribosome-profiling","display_name":"ribosome profiling","score":0.996999979019165},{"id":"https://openalex.org/keywords/alternative-translation-start-sites","display_name":"alternative translation start sites","score":0.902999997138977},{"id":"https://openalex.org/keywords/protein-identification","display_name":"protein identification","score":0.8600000143051147},{"id":"https://openalex.org/keywords/bottom-up-proteomics","display_name":"shotgun proteomics","score":0.9390000104904175},{"id":"https://openalex.org/keywords/human-cancer-cell-lines","display_name":"human cancer cell lines","score":0.7590000033378601},{"id":"https://openalex.org/keywords/genetic-variation","display_name":"genetic variation","score":0.41100001335144043}],"concepts":[{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.9073296785354614},{"id":"https://openalex.org/C68289359","wikidata":"https://www.wikidata.org/wiki/Q7502514","display_name":"Shotgun proteomics","level":4,"score":0.7767613530158997},{"id":"https://openalex.org/C182325514","wikidata":"https://www.wikidata.org/wiki/Q7322425","display_name":"Ribosome profiling","level":5,"score":0.7439123392105103},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.73029625415802},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.693356990814209},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6856685280799866},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5697256922721863},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.547213613986969},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.497409850358963},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.49516621232032776},{"id":"https://openalex.org/C94795543","wikidata":"https://www.wikidata.org/wiki/Q3813754","display_name":"Human proteome project","level":4,"score":0.436073899269104},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37467294931411743},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24674034118652344},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.17842528223991394},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17316854000091553},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12747377157211304}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D045325","descriptor_name":"HCT116 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1002/pmic.201400180","doi":"https://doi.org/10.1002/pmic.201400180","is_oa":true,"landing_page_url":"https://doi.org/10.1002/pmic.201400180","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.201400180","source":{"id":"https://openalex.org/S182655450","display_name":"PROTEOMICS","issn_l":"1615-9853","issn":["1615-9853","1615-9861"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PROTEOMICS","raw_type":"journal-article"},{"id":"pmid:25156699","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25156699","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":"Proteomics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4391000","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4391000","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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Proteomics","raw_type":"Text"},{"id":"pmh:oai:archive.ugent.be:5822064","doi":null,"is_oa":false,"landing_page_url":"https://biblio.ugent.be/publication/5822064","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1615-9853","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1002/pmic.201400180","doi":"https://doi.org/10.1002/pmic.201400180","is_oa":true,"landing_page_url":"https://doi.org/10.1002/pmic.201400180","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.201400180","source":{"id":"https://openalex.org/S182655450","display_name":"PROTEOMICS","issn_l":"1615-9853","issn":["1615-9853","1615-9861"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PROTEOMICS","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G583046263","display_name":"Detailed analysis of the substrates and the specificity of the N-terminalacetyltransferases","funder_award_id":"G.0440.10","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G6535510228","display_name":"Complementary use of ribosome profiling and positional proteomics for mapping the translation initiation and nascent protein modification landscape in human cell lines","funder_award_id":"G.0269.13N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G701551177","display_name":"AT-less Type I Polyketide Synthases","funder_award_id":"R01CA106150","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2014201551.pdf","grobid_xml":"https://content.openalex.org/works/W2014201551.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1481679225","https://openalex.org/W1536886974","https://openalex.org/W1839478134","https://openalex.org/W1966168891","https://openalex.org/W1975847255","https://openalex.org/W1981593008","https://openalex.org/W1988163167","https://openalex.org/W1994244877","https://openalex.org/W2007019025","https://openalex.org/W2010005720","https://openalex.org/W2010651323","https://openalex.org/W2019050932","https://openalex.org/W2019158910","https://openalex.org/W2020541351","https://openalex.org/W2022873228","https://openalex.org/W2024751967","https://openalex.org/W2024954384","https://openalex.org/W2032601646","https://openalex.org/W2033492309","https://openalex.org/W2042228684","https://openalex.org/W2045022080","https://openalex.org/W2045440227","https://openalex.org/W2047275456","https://openalex.org/W2051810299","https://openalex.org/W2057761395","https://openalex.org/W2057850601","https://openalex.org/W2058322072","https://openalex.org/W2058977593","https://openalex.org/W2063987069","https://openalex.org/W2065566217","https://openalex.org/W2071849521","https://openalex.org/W2079563665","https://openalex.org/W2081347927","https://openalex.org/W2081557520","https://openalex.org/W2085928374","https://openalex.org/W2091528429","https://openalex.org/W2095032938","https://openalex.org/W2098900123","https://openalex.org/W2100424218","https://openalex.org/W2107578201","https://openalex.org/W2108539496","https://openalex.org/W2112226798","https://openalex.org/W2122064342","https://openalex.org/W2127379559","https://openalex.org/W2128016314","https://openalex.org/W2128551987","https://openalex.org/W2130706354","https://openalex.org/W2133465414","https://openalex.org/W2133968430","https://openalex.org/W2140946052","https://openalex.org/W2148490163","https://openalex.org/W2148853951","https://openalex.org/W2152645648","https://openalex.org/W2165423269","https://openalex.org/W2165962849","https://openalex.org/W2166810745","https://openalex.org/W2167540700","https://openalex.org/W4244736178"],"related_works":["https://openalex.org/W2122064342","https://openalex.org/W2246563640","https://openalex.org/W2095520216","https://openalex.org/W2267165345","https://openalex.org/W2124779706","https://openalex.org/W4401450197","https://openalex.org/W6920724454","https://openalex.org/W2526901587","https://openalex.org/W2751539618","https://openalex.org/W2045022080"],"abstract_inverted_index":{"Next-generation":[0],"transcriptome":[1,19],"sequencing":[2,37],"is":[3,32],"increasingly":[4],"integrated":[5],"with":[6,23,160],"MS":[7],"to":[8,58,92,98,168],"enhance":[9],"MS-based":[10,180],"protein":[11,50,65,181],"and":[12,88,112,124,147,157,182,185],"peptide":[13,183],"identification.":[14],"Recently,":[15],"a":[16,63,75,80,149,161,193],"breakthrough":[17],"in":[18,48,129,142],"analysis":[20],"was":[21,96],"achieved":[22],"the":[24,35,44,53,60,118,130,143,152,174],"development":[25],"of":[26,38,47,62,108,121,155,176],"ribosome":[27,93,177],"profiling":[28,178],"(ribo-seq).":[29],"This":[30],"technology":[31],"based":[33],"on":[34,69,79],"deep":[36],"ribosome-protected":[39],"mRNA":[40],"fragments,":[41],"thereby":[42],"enabling":[43],"direct":[45],"observation":[46],"vivo":[49],"synthesis":[51],"at":[52],"transcript":[54],"level.":[55],"In":[56],"order":[57],"explore":[59],"impact":[61],"ribo-seq-derived":[64],"sequence":[66],"search":[67],"space":[68],"MS/MS":[70],"spectrum":[71],"identification,":[72],"we":[73,134,186],"performed":[74],"comprehensive":[76],"proteome":[77],"study":[78,172],"human":[81],"cancer":[82],"cell":[83],"line,":[84],"using":[85],"both":[86],"shotgun":[87,131,158],"N-terminal":[89,144],"proteomics,":[90],"next":[91],"profiling,":[94],"which":[95],"used":[97],"delineate":[99],"(alternative)":[100],"translational":[101],"reading":[102],"frames.":[103],"By":[104],"including":[105],"protein-level":[106],"evidence":[107],"sample-specific":[109],"genetic":[110],"variation":[111],"alternative":[113,138],"translation,":[114],"this":[115,171,188],"strategy":[116],"improved":[117],"identification":[119,184],"score":[120],"69":[122],"proteins":[123,128],"identified":[125],"22":[126],"new":[127,137],"experiment.":[132],"Furthermore,":[133],"discovered":[135],"18":[136],"translation":[139],"start":[140],"sites":[141],"proteomics":[145,159],"data":[146],"observed":[148],"correlation":[150,163],"between":[151],"quantitative":[153],"measures":[154],"ribo-seq":[156],"Pearson":[162],"coefficient":[164],"ranging":[165],"from":[166],"0.483":[167],"0.664.":[169],"Overall,":[170],"demonstrated":[173],"benefits":[175],"for":[179,196],"believe":[187],"approach":[189],"could":[190],"develop":[191],"into":[192],"common":[194],"practice":[195],"next-generation":[197],"proteomics.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":3}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}