Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

(2017) George Rosenberger et al.   NATURE METHODS

Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction

(2016) I. Ortea et al.   Journal of Proteomics

Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources

(2016) Joao A. Paulo et al.   Journal of Proteomics

Global Analysis of Host and Bacterial Ubiquitinome in Response to Salmonella Typhimurium Infection

(2016) Evgenij Fiskin et al.   MOLECULAR CELL

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

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

A comprehensive compilation of SUMO proteomics

(2016) Ivo A. Hendriks et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Synaptic AMPA receptor composition in development, plasticity and disease

(2016) Jeremy M. Henley et al.   NATURE REVIEWS NEUROSCIENCE

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

(2016) Roland Bruderer et al.   PROTEOMICS

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

A draft map of the mouse pluripotent stem cell spatial proteome

(2016) Andy Christoforou et al.   Nature Communications

Understanding the dimorphic lifestyles of human gastric pathogen Helicobacter pylori using the SWATH-based proteomics approach

(2016) Mun Fai Loke et al.   Scientific Reports

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

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

(2015) Jan Muntel 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

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

(2015) Scarlet Beck et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury

(2015) Hasmik Keshishian 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

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative variability of 342 plasma proteins in a human twin population

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

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

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

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Cell-Type-Resolved Quantitative Proteomics of Murine Liver

(2014) S. Babak Azimifar et al.   Cell Metabolism

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

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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Global analysis of protein structural changes in complex proteomes

(2014) Yuehan Feng et al.   NATURE BIOTECHNOLOGY

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

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

(2014) George Rosenberger et al.   Scientific Data

Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

(2013) Huisong Pak et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The One Hour Yeast Proteome

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

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

(2013) Ute Distler 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

In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are modulated by sensory deprivation

(2013) M. T. Butko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples

(2012) Scott J. Geromanos et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Development and critical period plasticity of the barrel cortex

(2012) Reha S. Erzurumlu et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

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

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger 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

Direct identification of ligand-receptor interactions on living cells and tissues

(2012) Andreas P Frei et al.   NATURE BIOTECHNOLOGY

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

(2011) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Genomewide Analysis of Rat Barrel Cortex Reveals Time- and Layer-Specific mRNA Expression Changes Related to Experience-Dependent Plasticity

(2011) A. Valles et al.   JOURNAL OF NEUROSCIENCE

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

(2011) J. Zhang et al.   Molecular Systems Biology

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

(2011) Lukas Reiter et al.   NATURE METHODS

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

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

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

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

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

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Modification-specific proteomics: Strategies for characterization of post-translational modifications using enrichment techniques

(2009) Yingming Zhao et al.   PROTEOMICS

Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures

(2009) Guo-Zhong Li et al.   PROTEOMICS

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS

(2009) Scott J. Geromanos et al.   PROTEOMICS

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

Erratum: Corrigendum: Identification of cross-linked peptides from large sequence databases

(2008) Oliver Rinner et al.   NATURE METHODS