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Here, by combining a novel bioinformatics tool (RanSEPs) with \u201c\u2010omics\u201d approaches, we were able to describe 109 bacterial small ORFomes. Predictions were first validated by performing an exhaustive search of SEPs present in\n                    <jats:italic>Mycoplasma pneumoniae<\/jats:italic>\n                    proteome via mass spectrometry, which illustrated the limitations of shotgun approaches. Then, RanSEPs predictions were validated and compared with other tools using proteomic datasets from different bacterial species and SEPs from the literature. We found that up to 16\u00a0\u00b1\u00a09% of proteins in an organism could be classified as SEPs. Integration of RanSEPs predictions with transcriptomics data showed that some annotated non\u2010coding RNAs could in fact encode for SEPs. A functional study of SEPs highlighted an enrichment in the membrane, translation, metabolism, and nucleotide\u2010binding categories. Additionally, 9.7% of the SEPs included a N\u2010terminus predicted signal peptide. We envision RanSEPs as a tool to unmask the hidden universe of small bacterial proteins.\n                  <\/jats:p>","DOI":"10.15252\/msb.20188290","type":"journal-article","created":{"date-parts":[[2019,2,22]],"date-time":"2019-02-22T10:55:20Z","timestamp":1550832920000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":127,"title":["Unraveling the hidden universe of small proteins in bacterial genomes"],"prefix":"10.1038","volume":"15","author":[{"given":"Samuel","family":"Miravet\u2010Verde","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tony","family":"Ferrar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guadalupe","family":"Espadas\u2010Garc\u00eda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rocco","family":"Mazzolini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anas","family":"Gharrab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduard","family":"Sabido","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Serrano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7568-4353","authenticated-orcid":false,"given":"Maria","family":"Lluch\u2010Senar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,2,22]]},"reference":[{"key":"BFMSB188290_CR1","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1038\/sj.emboj.7601983","volume":"27","author":"E Alix","year":"2008","unstructured":"Alix E, Blanc\u2010Potard A\u2010B (2008) Peptide\u2010assisted degradation of the Salmonella MgtC virulence factor. 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