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Quick microbial molecular phenotyping by differential shotgun proteomics
Author(s) -
Gouveia Duarte,
Grenga Lucia,
Pible Olivier,
Armengaud Jean
Publication year - 2020
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.14975
Subject(s) - shotgun proteomics , shotgun , biology , proteomics , computational biology , proteome , microorganism , shotgun sequencing , bacteria , bioinformatics , genetics , genome , gene
Summary Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied to study (i) specific microorganisms subjected to a variety of growth or stress conditions or (ii) different microorganisms sampled in the same condition. In microbiology, this comparison is particularly successful because differing microorganism phenotypes are explained by clearly altered abundances of key protein players. The extensive description and quantification of proteins from any given microorganism can be routinely obtained for several conditions within a few days by tandem mass spectrometry. Such protein‐centred microbial molecular phenotyping is rich in information. However, well‐designed experimental strategies, carefully parameterized analytical pipelines, and sound statistical approaches must be applied if the shotgun proteomic data are to be correctly interpreted. This minireview describes these key items for a quick molecular phenotyping based on label‐free quantification shotgun proteomics.