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. 2017 May 23;18:402. doi: 10.1186/s12864-017-3800-9

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© The Author(s). 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Experimental identification and bioinformatics analysis workflow of the proteogenomics study. Whole cell protein and membrane protein extracts were prepared from B. abortus 104 M cultures grown to exponential phase. Complexity reduction was achieved by SDS-PAGE and SCX HPLC separation. After protein extraction and pre-fractionation, enzymatically digested proteins or peptides were analyzed by LC-MS/MS. All spectra were searched against the six-frame (6 F) database and the UniProt database by SearchGUI. Identified peptides were mapped to the 104 M genome and annotation was refined at three levels: (i) confirmation of the existing open reading frame (ORF) models; (ii) refinement of the existing ORF models; and (iii) identification of novel ORF models. Subsequently, the protein physical\chemical property and function were analyzed