{"id":"https://openalex.org/W3163767187","doi":"https://doi.org/10.1093/nar/gkab368","title":"PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics","display_name":"PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics","publication_year":2021,"publication_date":"2021-04-25","ids":{"openalex":"https://openalex.org/W3163767187","doi":"https://doi.org/10.1093/nar/gkab368","mag":"3163767187","pmid":"https://pubmed.ncbi.nlm.nih.gov/33999207"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkab368","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab368","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W510/38841731/gkab368.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","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/nar/article-pdf/49/W1/W510/38841731/gkab368.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072969883","display_name":"Muhammad Farhan Khalid","orcid":"https://orcid.org/0000-0003-0452-5149"},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Farhan Khalid","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049945141","display_name":"Kanzal Iman","orcid":null},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Kanzal Iman","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001155649","display_name":"Amna Ghafoor","orcid":null},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Amna Ghafoor","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007302268","display_name":"Mujtaba Saboor","orcid":null},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Mujtaba Saboor","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101957301","display_name":"Ahsan Ali","orcid":"https://orcid.org/0000-0002-7924-5451"},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Ahsan Ali","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004394596","display_name":"Urwa Muaz","orcid":null},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Urwa Muaz","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074551463","display_name":"Abdul Rehman Basharat","orcid":"https://orcid.org/0000-0002-4675-5375"},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Abdul Rehman Basharat","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":"https://orcid.org/0000-0002-4675-5375","affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108647372","display_name":"Taha Tahir","orcid":null},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Taha Tahir","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071281366","display_name":"Muhammad Abubakar","orcid":"https://orcid.org/0000-0001-6902-6549"},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Abubakar","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091316629","display_name":"Momina Amer Akhter","orcid":null},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Momina Amer Akhter","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075369228","display_name":"Syed Waqar Nabi","orcid":"https://orcid.org/0000-0003-3835-4851"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Waqar Nabi","raw_affiliation_strings":["School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047735250","display_name":"Wim Vanderbauwhede","orcid":"https://orcid.org/0000-0001-6768-0037"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wim Vanderbauwhede","raw_affiliation_strings":["School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102019161","display_name":"Fayyaz Ahmad","orcid":"https://orcid.org/0000-0002-6315-6710"},"institutions":[{"id":"https://openalex.org/I99165933","display_name":"University of Gujrat","ror":"https://ror.org/01xe5fb92","country_code":"PK","type":"education","lineage":["https://openalex.org/I99165933"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Fayyaz Ahmad","raw_affiliation_strings":["Department of Statistics, University of Gujrat, Gujrat, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Gujrat, Gujrat, Pakistan","institution_ids":["https://openalex.org/I99165933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051600305","display_name":"Bilal Wajid","orcid":"https://orcid.org/0000-0003-0220-7788"},"institutions":[{"id":"https://openalex.org/I142732210","display_name":"University of Engineering and Technology Lahore","ror":"https://ror.org/0051w2v06","country_code":"PK","type":"education","lineage":["https://openalex.org/I142732210"]},{"id":"https://openalex.org/I87482320","display_name":"University of Management and Technology","ror":"https://ror.org/0095xcq10","country_code":"PK","type":"education","lineage":["https://openalex.org/I87482320"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Bilal Wajid","raw_affiliation_strings":["Department of Computer Science, University of Management and Technology, Lahore, Pakistan","Department of Electrical Engineering, University of Engineering and Technology, Lahore,\u00a0Pakistan","Division of Research and Development, Sabz-Qalam, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Management and Technology, Lahore, Pakistan","institution_ids":["https://openalex.org/I87482320"]},{"raw_affiliation_string":"Department of Electrical Engineering, University of Engineering and Technology, Lahore,\u00a0Pakistan","institution_ids":["https://openalex.org/I142732210"]},{"raw_affiliation_string":"Division of Research and Development, Sabz-Qalam, Lahore, Pakistan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043191237","display_name":"Safee Ullah Chaudhary","orcid":"https://orcid.org/0000-0002-3758-6581"},"institutions":[{"id":"https://openalex.org/I207789805","display_name":"Lahore University of Management Sciences","ror":"https://ror.org/05b5x4a35","country_code":"PK","type":"education","lineage":["https://openalex.org/I207789805"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Safee Ullah Chaudhary","raw_affiliation_strings":["Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan"],"raw_orcid":"https://orcid.org/0000-0002-3758-6581","affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan","institution_ids":["https://openalex.org/I207789805"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5043191237"],"corresponding_institution_ids":["https://openalex.org/I207789805"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.5675,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.61443785,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"49","issue":"W1","first_page":"W510","last_page":"W515"},"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":0.9998000264167786,"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":0.9965999722480774,"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/computer-science","display_name":"Computer science","score":0.7890491485595703},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7165848016738892},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6282917857170105},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6143264174461365},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5954424738883972},{"id":"https://openalex.org/keywords/multilayer-perceptron","display_name":"Multilayer perceptron","score":0.5208221673965454},{"id":"https://openalex.org/keywords/perceptron","display_name":"Perceptron","score":0.5019054412841797},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.488484263420105},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.47569072246551514},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.4351036846637726},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39344853162765503},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3496604561805725},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33092671632766724},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.27412304282188416},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2033785581588745},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1563117802143097},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.14953547716140747}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7890491485595703},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7165848016738892},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6282917857170105},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6143264174461365},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5954424738883972},{"id":"https://openalex.org/C179717631","wikidata":"https://www.wikidata.org/wiki/Q2991667","display_name":"Multilayer perceptron","level":3,"score":0.5208221673965454},{"id":"https://openalex.org/C60908668","wikidata":"https://www.wikidata.org/wiki/Q690207","display_name":"Perceptron","level":3,"score":0.5019054412841797},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.488484263420105},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.47569072246551514},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.4351036846637726},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39344853162765503},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3496604561805725},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33092671632766724},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.27412304282188416},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2033785581588745},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1563117802143097},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.14953547716140747},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"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":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkab368","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab368","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W510/38841731/gkab368.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:33999207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33999207","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:eprints.gla.ac.uk:242060","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:8262694","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8262694","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,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkab368","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab368","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W510/38841731/gkab368.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G4137454606","display_name":null,"funder_award_id":"STG-BIO-1008","funder_id":"https://openalex.org/F4320307871","funder_display_name":"The World Academy of Sciences"},{"id":"https://openalex.org/G5030643988","display_name":null,"funder_award_id":"20-2269/NRPU/R&D/HEC/12/4792","funder_id":"https://openalex.org/F4320322799","funder_display_name":"Higher Education Commission, Pakistan"},{"id":"https://openalex.org/G6202005372","display_name":null,"funder_award_id":"20-3629/NRPU/R&D/HEC/14/585","funder_id":"https://openalex.org/F4320322799","funder_display_name":"Higher Education Commission, Pakistan"},{"id":"https://openalex.org/G7646388397","display_name":null,"funder_award_id":"RG 14-319 RG/ITC/AS_C","funder_id":"https://openalex.org/F4320307871","funder_display_name":"The World Academy of Sciences"},{"id":"https://openalex.org/G7823824018","display_name":null,"funder_award_id":"FIF-BIO-2052","funder_id":"https://openalex.org/F4320307871","funder_display_name":"The World Academy of Sciences"},{"id":"https://openalex.org/G8861213803","display_name":null,"funder_award_id":"FIF-BIO-0255","funder_id":"https://openalex.org/F4320307871","funder_display_name":"The World Academy of Sciences"},{"id":"https://openalex.org/G933317001","display_name":null,"funder_award_id":"21-320SRGP/R&D/HEC/2014","funder_id":"https://openalex.org/F4320322799","funder_display_name":"Higher Education Commission, Pakistan"}],"funders":[{"id":"https://openalex.org/F4320307871","display_name":"The World Academy of Sciences","ror":"https://ror.org/00twbd828"},{"id":"https://openalex.org/F4320322799","display_name":"Higher Education Commission, Pakistan","ror":"https://ror.org/038y3sz68"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W3163767187.pdf"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W152206097","https://openalex.org/W1568341953","https://openalex.org/W1836244824","https://openalex.org/W1981593008","https://openalex.org/W2023010129","https://openalex.org/W2027572771","https://openalex.org/W2054667035","https://openalex.org/W2061635752","https://openalex.org/W2110017950","https://openalex.org/W2115467721","https://openalex.org/W2122588871","https://openalex.org/W2131381861","https://openalex.org/W2138455910","https://openalex.org/W2146103026","https://openalex.org/W2146482199","https://openalex.org/W2286617058","https://openalex.org/W2462197865","https://openalex.org/W2741268114","https://openalex.org/W2743289556","https://openalex.org/W2966240335"],"related_works":["https://openalex.org/W2076543106","https://openalex.org/W2019891950","https://openalex.org/W2085842814","https://openalex.org/W4286643620","https://openalex.org/W2523437662","https://openalex.org/W4387048144","https://openalex.org/W2492135063","https://openalex.org/W2362514456","https://openalex.org/W2766585573","https://openalex.org/W4387490624"],"abstract_inverted_index":{"PERCEPTRON":[0,16,136],"is":[1,61,170],"a":[2],"next-generation":[3],"freely":[4],"available":[5,122,172,187],"web-based":[6],"proteoform":[7],"identification":[8,44],"and":[9,53,108,120,150,169],"characterization":[10,35],"platform":[11],"for":[12,22,93,102],"top-down":[13],"proteomics":[14],"(TDP).":[15],"search":[17,97,167],"pipeline":[18],"brings":[19],"together":[20],"algorithms":[21],"(i)":[23],"intact":[24],"protein":[25,57],"mass":[26],"tuning,":[27],"(ii)":[28],"de":[29],"novo":[30],"sequence":[31],"tags-based":[32],"filtering,":[33],"(iii)":[34],"of":[36,45,66,96,104,110,147,154,181],"terminal":[37],"as":[38,40,99,101],"well":[39,100],"post-translational":[41],"modifications,":[42],"(iv)":[43],"truncated":[46],"proteoforms,":[47],"(v)":[48],"in":[49,72,145,152,165],"silico":[50],"spectral":[51],"comparison,":[52],"(vi)":[54],"weight-based":[55],"candidate":[56],"scoring.":[58],"High-throughput":[59],"performance":[60,109],"achieved":[62],"through":[63],"the":[64,111,158,163,182,189],"execution":[65],"optimized":[67],"code":[68,186],"via":[69],"multiple":[70],"threads":[71],"parallel,":[73],"on":[74,116,188],"graphics":[75],"processing":[76],"units":[77],"(GPUs)":[78],"using":[79],"NVidia":[80],"Compute":[81],"Unified":[82],"Device":[83],"Architecture":[84],"(CUDA)":[85],"framework.":[86],"An":[87],"intuitive":[88],"graphical":[89],"web":[90],"interface":[91],"allows":[92],"setting":[94],"up":[95,142],"parameters":[98],"visualization":[103],"results.":[105],"The":[106],"accuracy":[107],"tool":[112,160,183],"have":[113],"been":[114],"validated":[115],"several":[117],"TDP":[118,123,132,166],"datasets":[119,133],"against":[121],"software.":[124],"Specifically,":[125],"results":[126],"obtained":[127],"from":[128],"searching":[129],"two":[130],"published":[131],"demonstrate":[134],"that":[135],"outperforms":[137],"all":[138],"other":[139],"tools":[140],"by":[141,184],"to":[143],"135%":[144],"terms":[146,153],"reported":[148],"proteins":[149],"10-fold":[151],"runtime.":[155],"In":[156],"conclusion,":[157],"proposed":[159],"significantly":[161],"enhances":[162],"state-of-the-art":[164],"software":[168],"publicly":[171],"at":[173],"https://perceptron.lums.edu.pk.":[174],"Users":[175],"can":[176],"also":[177],"create":[178],"in-house":[179],"deployments":[180],"building":[185],"GitHub":[190],"repository":[191],"(http://github.com/BIRL/Perceptron).":[192]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}
