High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation

specL—an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics

(2015) Christian Panse et al.   BIOINFORMATICS

Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer

(2015) Jan Muntel et al.   JOURNAL OF PROTEOME RESEARCH

Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry

(2015) Kimberly A. Krautkramer et al.   JOURNAL OF PROTEOME RESEARCH

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

(2015) Ying S. Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2015) Sarah J. Parker et al.   MOLECULAR & CELLULAR PROTEOMICS

Reproducible and Consistent Quantification of theSaccharomyces cerevisiaeProteome by SWATH-mass spectrometry

(2015) Nathalie Selevsek et al.   MOLECULAR & CELLULAR PROTEOMICS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

(2015) Tiannan Guo et al.   NATURE MEDICINE

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

(2015) Jian Wang et al.   NATURE METHODS

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Building high-quality assay libraries for targeted analysis of SWATH MS data

(2015) Olga T Schubert et al.   Nature Protocols

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

(2014) Richard Alexander Scheltema et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Mass spectrometric protein maps for biomarker discovery and clinical research

(2013) Yansheng Liu et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup 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

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

(2012) Claudia Escher et al.   PROTEOMICS

Faster, Quantitative, and Accurate Precursor Acquisition Independent From Ion Count

(2011) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Lukas Reiter et al.   NATURE METHODS

XDIA: improving on the label-free data-independent analysis

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

(2010) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometry in high-throughput proteomics: ready for the big time

(2010) Tommy Nilsson et al.   NATURE METHODS

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

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Deconvolution of Mixture Spectra from Ion-Trap Data-Independent-Acquisition Tandem Mass Spectrometry

(2009) Marshall Bern et al.   ANALYTICAL CHEMISTRY

Targeted proteomic strategy for clinical biomarker discovery

(2008) Ralph Schiess et al.   Molecular Oncology