MS analysis of B. nonstop proteins

•Mascot error tolerant (Mascot server) search and dependent peptides search (MaxQuant) has been done •Mascot •2nd replicate search used only •takes into account whole protein sequences of identified proteins and searches them with relaxed search conditions like semispecific enzyme specificity, all modifications etc. •MaxQuant •all replicates were used •takes into account identified peptides and searches them with all set modifications •search results filtering •Mascot: ion score >20 •8652 peptide spectrum matches used after the filtration •MaxQuant: PEP •25961 peptide features (3D peaks in the LC-MS profile) used after the filtration