Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline

(2018) Vagisha Sharma et al.   MOLECULAR & CELLULAR PROTEOMICS

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

(2018) Brian C. Searle et al.   Nature Communications

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

(2017) Meena Choi et al.   JOURNAL OF PROTEOME RESEARCH

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences

(2017) Bo Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

(2015) Guoshou Teo et al.   Journal of Proteomics

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet

(2015) Andrew Keller 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

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

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

Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomics

(2015) Tom Dunkley et al.   Proteomics Clinical Applications

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

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

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

(2011) Lukas Reiter et al.   NATURE METHODS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry

(2009) S. E. Abbatiello et al.   CLINICAL CHEMISTRY

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