Large scale analysis of amino acid substitutions in bacterial proteomics

BMC Bioinformatics

Research Article

Ivan Butenko¹  Andrey Larin¹  Elena Ilina¹  Olga Pobeguts¹  Egor Shitikov¹  Maja Malakhova¹  Nikolay Anikanov¹  Elena Kostryukova¹  Sergey Kovalchuk¹  Vadim Govorun¹  Ilya Altukhov²  Dmitry Alexeev²  Dmitry Ischenko²  Alexandra Kanygina² 

[1] Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, 119435, Moscow, Russian Federation;Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, 119435, Moscow, Russian Federation;Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, 141700, Dolgoprudny, Russian Federation;

关键词: Spectral library;    SAP;   

DOI  :  10.1186/s12859-016-1301-5

 received in 2016-07-05, accepted in 2016-10-21,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundProteomics 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.ResultsHere 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.ConclusionThe 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.

【 授权许可】

CC BY   
© The Author(s) 2016

【 图 表 】

Fig. 6