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Previous proteome and transcriptome studies of <jats:italic>Neisseria\u00a0meningitidis<\/jats:italic> have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed\u2010phase liquid chromatography combined with data\u2010independent alternate scanning mass spectrometry (<jats:styled-content style=\"fixed-case\">LC<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">MS<jats:sup>E<\/jats:sup><\/jats:styled-content>) was utilized for rapid high\u2010resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal <jats:italic>hfq<\/jats:italic> deletion mutant. Whole\u2010cell lysates of <jats:italic>N.\u00a0meningitidis<\/jats:italic> serogroup B H44\/76 wild\u2010type (wt) and H44\/76\u0394<jats:italic>hfq<\/jats:italic> (\u0394<jats:italic>hfq<\/jats:italic>) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by liquid chromatography (<jats:styled-content style=\"fixed-case\">LC<\/jats:styled-content>) prior to analysis by mass spectrometry (<jats:styled-content style=\"fixed-case\">MS<jats:sup>E<\/jats:sup><\/jats:styled-content>). Differential expression was analyzed by Student's <jats:italic>t<\/jats:italic>\u2010test with control for false discovery rate (<jats:styled-content style=\"fixed-case\">FDR<\/jats:styled-content>). Reliable quantitation of relative expression comparing wt and \u0394<jats:italic>hfq<\/jats:italic> was achieved with 506 proteins (20%). Upon <jats:styled-content style=\"fixed-case\">FDR<\/jats:styled-content> control at <jats:italic>q\u00a0<\/jats:italic>\u2264<jats:italic>\u00a0<\/jats:italic>0.05, 48 up\u2010 and 59 downregulated proteins were identified. From these, 81 were identified as novel Hfq\u2010regulated candidates, while 15 proteins were previously found by <jats:styled-content style=\"fixed-case\">SDS<\/jats:styled-content>\/<jats:styled-content style=\"fixed-case\">PAGE<\/jats:styled-content>\/<jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content> and 24 with microarray analyses. Thus, using <jats:styled-content style=\"fixed-case\">LC<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">MS<jats:sup>E<\/jats:sup><\/jats:styled-content> we have expanded the repertoire of Hfq\u2010regulated proteins. In conjunction with previous studies, a comprehensive network of Hfq\u2010regulated proteins was constructed and differentially expressed proteins were found to be involved in a large variety of cellular processes. The results and comparisons with other gram\u2010negative model systems, suggest still unidentified <jats:styled-content style=\"fixed-case\">sRNA<\/jats:styled-content> analogs in <jats:italic>N.\u00a0meningitidis<\/jats:italic>.<\/jats:p>","DOI":"10.1002\/2211-5463.12218","type":"journal-article","created":{"date-parts":[[2017,3,16]],"date-time":"2017-03-16T07:32:46Z","timestamp":1489649566000},"page":"777-788","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["The Hfq regulon of <i>Neisseria\u00a0meningitidis<\/i>"],"prefix":"10.1002","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6401-6763","authenticated-orcid":false,"given":"Robert A. 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