DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

Intelligent Data Acquisition Blends Targeted and Discovery Methods

(2014) Derek J. Bailey et al.   JOURNAL OF PROTEOME RESEARCH

Numerical Compression Schemes for Proteomics Mass Spectrometry Data

(2014) Johan Teleman et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Segmentation of Precursor Mass Range Using “Tiling” Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification

(2013) Catherine E. Vincent et al.   ANALYTICAL CHEMISTRY

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

Automated Selected Reaction Monitoring Software for Accurate Label-Free Protein Quantification

(2012) Johan Teleman et al.   JOURNAL OF PROTEOME RESEARCH

Protein Expression Changes in Ovarian Cancer during the Transition from Benign to Malignant

(2012) Sofia Waldemarson et al.   JOURNAL OF PROTEOME RESEARCH

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

(2012) Chad R. Weisbrod et al.   JOURNAL OF PROTEOME RESEARCH

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

(2012) Christofer Karlsson et al.   Nature Communications

Streptococcus pyogenesin Human Plasma

(2011) Johan Malmström et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification

(2011) Sven Nahnsen et al.   JOURNAL OF PROTEOME RESEARCH

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists

(2011) Eric W. Deutsch et al.   MOLECULAR & CELLULAR PROTEOMICS

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data

(2009) Jari Häkkinen et al.   JOURNAL OF PROTEOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH