Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry

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

(2014) Johan Teleman et al.   BIOINFORMATICS

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis

(2013) Olga T. Schubert et al.   Cell Host & Microbe

Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome

(2013) Víctor Segura et al.   JOURNAL OF PROTEOME RESEARCH

Maximizing Peptide Identification Events in Proteomic Workflows Using Data-Dependent Acquisition (DDA)

(2013) Nicholas W. Bateman et al.   MOLECULAR & CELLULAR PROTEOMICS

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

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

(2013) Ben C Collins et al.   NATURE METHODS

Quantitative measurements ofN-linked glycoproteins in human plasma by SWATH-MS

(2013) Yansheng Liu et al.   PROTEOMICS

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

(2012) Hannes Röst et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Highly multiplexed targeted proteomics using precise control of peptide retention time

(2012) Sebastien Gallien et al.   PROTEOMICS

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

(2012) Claudia Escher et al.   PROTEOMICS

Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

(2012) R. Huttenhain et al.   Science Translational Medicine

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

(2012) Christofer Karlsson et al.   Nature Communications

Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics

(2011) Henry Lam et al.   METHODS

Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach

(2009) Nico Pfeifer et al.   JOURNAL OF PROTEOME RESEARCH