Host-centric proteomics of stool

Soluble extra-cellular proteins and peptides from human and mouse stool were fractionated on a C-4 solid phase extraction cartidge, trypsin digested, C-18 clean up and identified with MS/MS on a LTQ-Velos Orbitrap. Data processing: The readRAW program was used to generate peak lists from the original data. All protein sequences were reversed and concatenated to the original forward-oriented proteins. Spectra were assigned to peptides using a semi-specific enzyme specificity with the Mascot search algorithm (version 2.3.01) using static carbamidomethylation of cysteines, differential oxidized methionines, 50ppm precursor mass tolerance, 2 miscleavages and 0.8Da fragment ion tolerance. Searched against a mouse or human database.