Large scale analysis of amino acid substitutions in bacterial proteomics

被引：3

作者：

Ischenko, Dmitry ^{[1
,2
]}

Alexeev, Dmitry ^{[1
,2
]}

Shitikov, Egor ^{[1
]}

Kanygina, Alexandra ^{[1
]}

Malakhova, Maja ^{[1
,2
]}

Kostryukova, Elena ^{[1
]}

Larin, Andrey ^{[1
]}

Kovalchuk, Sergey ^{[1
]}

Pobeguts, Olga ^{[1
]}

Butenko, Ivan ^{[1
]}

Anikanov, Nikolay ^{[1
]}

Altukhov, Ilya ^{[1
]}

Ilina, Elena ^{[1
]}

Govorun, Vadim ^{[1
]}

机构：

[1] Res Inst Phys Chem Med, Malaya Pirogovskaya 1a, Moscow 119435, Russia

[2] Moscow Inst Phys & Technol, Inst Pereulok 9, Dolgoprudnyi 141700, Russia

来源：

BMC BIOINFORMATICS | 2016年 / 17卷

基金：

俄罗斯科学基金会;

关键词：

Spectral library; SAP; POSTTRANSLATIONAL MODIFICATIONS; PEPTIDE IDENTIFICATION; VARIANT PEPTIDES; SEARCH; PROTEINS; SPECTRA; TANDEM;

D O I：

10.1186/s12859-016-1301-5

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：10

共 28 条

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