{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T08:04:19Z","timestamp":1782288259165,"version":"3.54.5"},"reference-count":6,"publisher":"Wiley","issue":"S1","license":[{"start":{"date-parts":[[2023,1,3]],"date-time":"2023-01-03T00:00:00Z","timestamp":1672704000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["302420\/2017\u20107"],"award-info":[{"award-number":["302420\/2017\u20107"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2019\/09464\u20106"],"award-info":[{"award-number":["2019\/09464\u20106"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Rapid Comm Mass Spectrometry"],"published-print":{"date-parts":[[2024,1]]},"abstract":"\n Rationale<\/jats:title>\n Discovery proteomics has been popularized to be essential in the investigator's biological toolbox. Many biological problems involve the interplay of multiple organisms. Herein, a bottom\u2010up proteomics workflow was developed to study a system containing multiple organisms to promote a thorough understanding of how each interacts with the others.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n A label\u2010free quantification proteomics workflow was developed with nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC\u2010MS\/MS). This protocol describes a bottom\u2010up proteomics workflow used to study differential protein expression in the context of fleas (\n Ctenocephalides felis felis<\/jats:italic>\n ) experimentally infected by the bacterium\n \n Bartonella henselae<\/jats:italic>\n <\/jats:styled-content>\n , the etiological agent of Cat Scratch Disease (CSD).\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Step\u2010by\u2010step instructions are provided for protein extraction, protein cleanup, total protein measurement, nanoLC\u2010MS\/MS data acquisition, and data analysis using Proteome Discoverer software. Comprehensive and exhaustive details are included to promote the adoption of this proteomics workflow in other laboratories.<\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n A proteomics protocol is detailed for a system containing multiple proteomes from different taxonomic lineages using CSD (cats bitten by fleas infected with\n Bartonella henselae<\/jats:italic>\n ) as a model. The operating protocol can be readily applied to other label\u2010free proteomics work involving multiple proteomes from taxonomically distinct organisms.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1002\/rcm.9431","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T15:42:29Z","timestamp":1669304549000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A bottom\u2010up proteomics workflow for a system containing multiple organisms"],"prefix":"10.1002","volume":"38","author":[{"given":"Hongxia","family":"Bai","sequence":"first","affiliation":[{"name":"Department of Chemistry North Carolina State University Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonard B.","family":"Collins","sequence":"additional","affiliation":[{"name":"Molecular Education, Technology and Research Innovation Center North Carolina State University Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcos Rog\u00e9rio","family":"Andr\u00e9","sequence":"additional","affiliation":[{"name":"Laboratory of Immunoparasitology, Department of Pathology, Reproduction and One Health, Faculdade de Ci\u00eancias Agr\u00e1rias e Veterin\u00e1rias Universidade Estadual Paulista Jaboticabal SP Brazil"},{"name":"Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine North Carolina State University Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward B.","family":"Breitschwerdt","sequence":"additional","affiliation":[{"name":"Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine North Carolina State University Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5838-4647","authenticated-orcid":false,"given":"Taufika Islam","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Chemistry North Carolina State University Raleigh North Carolina USA"},{"name":"Molecular Education, Technology and Research Innovation Center North Carolina State University Raleigh North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,1,3]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.828082"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1476\u20104431.2009.00496.x"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2021.05.008"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071\u2010018\u20102618\u2010x"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1322"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ab.2013.10.024"}],"container-title":["Rapid Communications in Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/rcm.9431","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/rcm.9431","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/rcm.9431","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T16:25:34Z","timestamp":1761495934000},"score":1,"resource":{"primary":{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/10.1002\/rcm.9431"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,3]]},"references-count":6,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2024,1]]}},"alternative-id":["10.1002\/rcm.9431"],"URL":"https:\/\/doi.org\/10.1002\/rcm.9431","archive":["Portico"],"relation":{},"ISSN":["0951-4198","1097-0231"],"issn-type":[{"value":"0951-4198","type":"print"},{"value":"1097-0231","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,3]]},"assertion":[{"value":"2022-09-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-01-03","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e9431"}}