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

J Proteome Res. 2018 Sep 7;17(9):2978-2986. doi: 10.1021/acs.jproteome.8b00166. Epub 2018 Aug 8.


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.

Keywords: ComPIL; MudPIT; membrane proteins; metaproteomics; microbiome; triflic acid.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacillus subtilis / chemistry*
  • Bacillus subtilis / genetics
  • Bacillus subtilis / metabolism
  • Bacterial Proteins / isolation & purification*
  • Chromatography, Liquid
  • Complex Mixtures / chemistry
  • Gastrointestinal Microbiome / genetics
  • Humans
  • Jurkat Cells
  • Membrane Proteins / isolation & purification*
  • Mesylates / chemistry*
  • Metagenome
  • Proteomics / methods*
  • Pseudomonas aeruginosa / chemistry*
  • Pseudomonas aeruginosa / genetics
  • Pseudomonas aeruginosa / metabolism
  • Sonication / methods
  • Tandem Mass Spectrometry


  • Bacterial Proteins
  • Complex Mixtures
  • Membrane Proteins
  • Mesylates
  • trifluoromethanesulfonic acid