Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.

ABSTRACT: LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw data processing, which utilizes precursor-level high mass accuracy data for peak processing and MGF creation. In particular, ProteinPilot results from MaxQuant-processed peaklists for Orbitrap 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 (ProteoMiner) treated whole saliva data set comprising 200 fractions. ProteinPilot's ability to simultaneously predict multiple modifications showed an advantage from ProteoMiner treatment for modified p

SUBMITTER: Jagtap P 

PROVIDER: S-EPMC3618284 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature