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.


CONCLUSIONS
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.
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation. dmitry.ischenko@phystech.edu.|Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation. dmitry.ischenko@phystech.edu.
Dmitry
D
Ischenko
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.|Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation.
Dmitry
D
Alexeev
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Egor
E
Shitikov
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.|Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation.
Alexandra
A
Kanygina
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Maja
M
Malakhova
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Elena
E
Kostryukova
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Andrey
A
Larin
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Sergey
S
Kovalchuk
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Olga
O
Pobeguts
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Ivan
I
Butenko
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Nikolay
N
Anikanov
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.|Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation.
Ilya
I
Altukhov
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Elena
E
Ilina
Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
Vadim
V
Govorun
D000465:Algorithms; D019943:Amino Acid Substitution; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism*; D030562:Databases, Protein; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D009154:Mutation / Q000235:genetics; D010446:Peptide Fragments / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods
D000596:Amino Acids; D001426:Bacterial Proteins; D010446:Peptide Fragments; D020543:Proteome
SAP; Spectral library