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

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...

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Bibliographic Details
Published in:Proteomics (Weinheim) 2012-06, Vol.12 (11), p.1726-1730
Main Authors: Jagtap, Pratik, Bandhakavi, Sricharan, Higgins, LeeAnn, McGowan, Thomas, Sa, Rongxiao, Stone, Matthew D., Chilton, John, Arriaga, Edgar A., Seymour, Sean L., Griffin, Timothy J.
Format: Article
Language:English
Subjects:
Accuracy
Algorithms
Analytical, structural and metabolic biochemistry
Bioinformatics
Biological and medical sciences
Combined workflows
Computational Biology
Data processing
Databases, Protein
Descriptive statistics
Fundamental and applied biological sciences. Psychology
High precursor mass accuracy and peaklist quality
Ions
Lasers
Mass Spectrometry
Miscellaneous
Proteins
Proteome
Proteomics - methods
Salivary Proteins and Peptides - analysis
Salivary Proteins and Peptides - chemistry
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Summary: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.
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.201100097