Large scale analysis of amino acid substitutions in bacterial proteomics
- Background: Proteomics of bacterial pathogens is a developing field exploring microbial physiology, gene expression and the complex interactions between bacteria and their hosts. One of the complications in proteomic approach is micro- and macro-heterogeneity of bacterial species, which makes it impossible to build a comprehensive database of bacterial genomes for identification, while most of the existing algorithms rely largely on genomic data. Results: Here we present a large scale study of identification of single amino acid polymorphisms between bacterial strains. An ad hoc method was developed based on MS/MS spectra comparison without the support of a genomic database. Whole-genome sequencing was used to validate the accuracy of polymorphism detection. Several approaches presented earlier to the proteomics community as useful for polymorphism detection were tested on isolates of Helicobacter pylori, Neisseria gonorrhoeae and Escherichia coli. Conclusion: The developed method represents a perspective approach in the field of bacterial proteomics allowing to identify hundreds of peptides with novel SAPs from a single proteome.
Author: | Dmitry Ischenko, Dmitry Alexeev, Egor Shitikov, Alexandra Kanygina, Maja Malakhova, Elena Kostryukova, Andrey Larin, Sergey Kovalchuk, Olga Pobeguts, Ivan Butenko, Nikolay Anikanov, Ilya Altukhov, Elena Ilina, Vadim Govorun |
---|---|
URN: | urn:nbn:de:hebis:30:3-447079 |
DOI: | https://doi.org/10.1186/s12859-016-1301-5 |
ISSN: | 1471-2105 |
Parent Title (English): | BMC Bioinformatics |
Publisher: | Berlin ; Heidelberg |
Place of publication: | Springer |
Document Type: | Article |
Language: | English |
Year of Completion: | 2016 |
Date of first Publication: | 2016/11/08 |
Publishing Institution: | Universitätsbibliothek Johann Christian Senckenberg |
Release Date: | 2017/10/27 |
Tag: | SAP; Spectral library |
Volume: | 17 |
Issue: | 450 |
Page Number: | 10 |
Note: | © The Author(s). 2016 Open Access This 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. |
HeBIS-PPN: | 446317322 |
Institutes: | Medizin / Medizin |
Dewey Decimal Classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit | |
Sammlungen: | Universitätspublikationen |
Licence (German): | Creative Commons - Namensnennung 4.0 |