Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass

The
lysis and extraction of soluble bacterial proteins from cells is a
common practice for proteomics analyses, but insoluble bacterial biomasses
are often left behind. Here, we show that with triflic acid treatment,
the insoluble bacterial biomass of Gram– and Gram+ bacteria can be rendered soluble. We use LC-MS/MS shotgun
proteomics to show that bacterial proteins in the soluble and insoluble
postlysis fractions differ significantly. Additionally, in the case
of Gram– Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell-envelope-associated
proteins. Finally, we apply triflic acid to a human microbiome sample
to show that this treatment is robust and enables the identification
of a new, complementary subset of proteins from a complex microbial
mixture.