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

Deep metaproteomic analysis of human salivary supernatant

(2012) Pratik Jagtap et al.   PROTEOMICS

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

A Dynamic Range Compression and Three-Dimensional Peptide Fractionation Analysis Platform Expands Proteome Coverage and the Diagnostic Potential of Whole Saliva

(2009) Sricharan Bandhakavi et al.   JOURNAL OF PROTEOME RESEARCH

Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

(2009) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses

(2009) Paul A. Rudnick et al.   MOLECULAR & CELLULAR PROTEOMICS

DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets

(2009) Vladislav A. Petyuk et al.   MOLECULAR & CELLULAR PROTEOMICS

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

(2009) Jürgen Cox et al.   Nature Protocols

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

(2009) Bernhard Y. Renard et al.   PROTEOMICS

Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data

(2008) Bingwen Lu et al.   ANALYTICAL CHEMISTRY

Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches

(2008) Wilfred H. Tang et al.   JOURNAL OF PROTEOME RESEARCH

Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies Peptide Identification by Database Retrieval

(2008) Michael T. Boyne et al.   JOURNAL OF PROTEOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Precision proteomics: The case for high resolution and high mass accuracy

(2008) M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA