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 <strong>whole protein sequences of identified proteins </strong>and searches them with relaxed search conditions like semispecific enzyme specificity, all modifications etc. •MaxQuant •all replicates were used •takes into account <strong>identified peptides </strong>and searches them with all set modifications •search results filtering •Mascot: ion score &gt;20 •8652 peptide spectrum matches used after the filtration •MaxQuant: PEP &lt;0.05 (i.e., local FDR 5%), peptide length difference = 0 •25961 peptide features (3D peaks in the LC-MS profile) used after the filtration