TY  - JOUR
A1  - Ischenko, Dmitry
A1  - Alexeev, Dmitry
A1  - Shitikov, Egor
A1  - Kanygina, Alexandra
A1  - Malakhova, Maja
A1  - Kostryukova, Elena
A1  - Larin, Andrey
A1  - Kovalchuk, Sergey
A1  - Pobeguts, Olga
A1  - Butenko, Ivan
A1  - Anikanov, Nikolay
A1  - Altukhov, Ilya
A1  - Ilina, Elena
A1  - Govorun, Vadim
T1  - Large scale analysis of amino acid substitutions in bacterial proteomics
T2  - BMC Bioinformatics
N2  - 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.
KW  - Spectral library
KW  - SAP
Y1  - 2016
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/44707
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-447079
SN  - 1471-2105
N1  - © 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.
VL  - 17
IS  - 450
PB  - Berlin ; Heidelberg
CY  - Springer
ER  -