Workflow for analysis of high mass accuracy salivary data set using M ax Q uant and P rotein P ilot search algorithm

LTQ O rbitrap data analyzed with P rotein P ilot can be further improved by M ax Q uant raw data processing, which utilizes precursor‐level high mass accuracy data for peak processing and MGF creation. In particular, P rotein P ilot results from M ax Q uant‐processed peaklists for O rbitrap data sets resulted in improved spectral utilization due to an improved peaklist quality with higher precision and high precursor mass accuracy ( HPMA ). The output and postsearch analysis tools of both workflows were utilized for previously unexplored features of a three‐dimensional fractionated and hexapeptide library ( P roteo M iner) treated whole saliva data set comprising 200 fractions. P rotein P ilot's ability to simultaneously predict multiple modifications showed an advantage from P roteo M iner treatment for modified peptide identification. We demonstrate that complementary approaches in the analysis pipeline provide comprehensive results for the whole saliva data set acquired on an LTQ O rbitrap. Overall our results establish a workflow for improved protein identification from high mass accuracy data.