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

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

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

Dynamic reciprocity: the role of annexin A2 in tissue integrity

(2014) Jessica K. Hitchcock et al.   Journal of Cell Communication and Signaling

Mass spectrometric protein maps for biomarker discovery and clinical research

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

Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring

(2013) Kai Pong Law et al.   Expert Review of Proteomics

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

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

Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome

(2013) Deborah Moran et al.   JOURNAL OF VIROLOGICAL METHODS

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

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

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Screening for Drug-Induced Hepatotoxicity in Primary Mouse Hepatocytes Using Acetaminophen, Amiodarone, and Cyclosporin A as Model Compounds: An Omics-Guided Approach

(2013) Anke Van Summeren et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Metabolism and Disposition of Acetaminophen: Recent Advances in Relation to Hepatotoxicity and Diagnosis

(2013) Mitchell R. McGill et al.   PHARMACEUTICAL RESEARCH

Multi-cell type human liver microtissues for hepatotoxicity testing

(2012) S. Messner et al.   ARCHIVES OF TOXICOLOGY

Normalization and missing value imputation for label-free LC-MS analysis

(2012) Yuliya V Karpievitch et al.   BMC BIOINFORMATICS

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

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

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

Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry

(2012) Michael A Gillette et al.   NATURE METHODS

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

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

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

(2011) Lukas Reiter et al.   NATURE METHODS

Pathophysiological Relevance of Proteomics Investigations of Drug-Induced Hepatotoxicity in HepG2 Cells

(2011) Hartmut Jaeschke et al.   TOXICOLOGICAL SCIENCES

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

Reduced Basal Autophagy and Impaired Mitochondrial Dynamics Due to Loss of Parkinson's Disease-Associated Protein DJ-1

(2010) Guido Krebiehl et al.   PLoS One

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg 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

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2009) Da Wei Huang et al.   Nature Protocols

Peroxiredoxin-6 protects against mitochondrial dysfunction and liver injury during ischemia-reperfusion in mice

(2008) Thorsten Eismann et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

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