title: 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 peptide identification. We demonstrate that complementary approaches in the analysis pipeline provide comprehensive results for the whole saliva data set acquired on an LTQ Orbitrap. Overall our results establish a workflow for improved protein identification from high mass accuracy data.
authors.affiliation: Minnesota Supercomputing Institute, Minneapolis, MN, USA. pratik@msi.umn.edu
authors.forename: Pratik
authors.initials: P
authors.lastname: Jagtap
authors.forename: Sricharan
authors.initials: S
authors.lastname: Bandhakavi
authors.forename: LeeAnn
authors.initials: L
authors.lastname: Higgins
authors.forename: Thomas
authors.initials: T
authors.lastname: McGowan
authors.forename: Rongxiao
authors.initials: R
authors.lastname: Sa
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Stone
authors.forename: John
authors.initials: J
authors.lastname: Chilton
authors.forename: Edgar A
authors.initials: EA
authors.lastname: Arriaga
authors.forename: Sean L
authors.initials: SL
authors.lastname: Seymour
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Griffin
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D013058:Mass Spectrometry; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012471:Salivary Proteins and Peptides / Q000032:analysis / Q000737:chemistry*
chemical_list: D020543:Proteome; D012471:Salivary Proteins and Peptides