Analysis ofDrosophila melanogasterproteome dynamics during embryonic development by a combination of label-free proteomics approaches

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

Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)

(2015) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments

(2015) Matthew J. Rardin et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics ofXenopusdevelopment

(2015) Liangliang Sun et al.   MOLECULAR HUMAN REPRODUCTION

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

Applications of targeted proteomics in systems biology and translational medicine

(2015) H. Alexander Ebhardt et al.   PROTEOMICS

Evaluation of iTRAQ and SWATH-MS for the Quantification of Proteins Associated with Insulin Resistance in Human Duodenal Biopsy Samples

(2015) Sylvie Bourassa et al.   PLoS One

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

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

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila

(2014) Carlo G. Artieri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrasensitive proteome analysis using paramagnetic bead technology

(2014) C. S. Hughes et al.   Molecular Systems Biology

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

A sentinel protein assay for simultaneously quantifying cellular processes

(2014) Martin Soste et al.   NATURE METHODS

Metabolome Analysis of Drosophila melanogaster during Embryogenesis

(2014) Phan Nguyen Thuy An et al.   PLoS One

Whole cell, label free protein quantitation with data independent acquisition: Quantitation at the MS2 level

(2014) Peter McQueen et al.   PROTEOMICS

miRISC recruits decapping factors to miRNA targets to enhance their degradation

(2013) T. Nishihara et al.   NUCLEIC ACIDS RESEARCH

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

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

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Subcellular Distribution and Dynamics of Active Proteasome Complexes Unraveled by a Workflow Combiningin VivoComplex Cross-Linking and Quantitative Proteomics

(2012) Bertrand Fabre et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien 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

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

The Drosophila Estrogen-Related Receptor Directs a Metabolic Switch that Supports Developmental Growth

(2011) Jason M. Tennessen et al.   Cell Metabolism

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Sphingosine-1-phosphate produced by sphingosine kinase 2 in mitochondria interacts with prohibitin 2 to regulate complex IV assembly and respiration

(2010) Graham M. Strub et al.   FASEB JOURNAL

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

In VivoStable Isotope Labeling of Fruit Flies Reveals Post-transcriptional Regulation in the Maternal-to-zygotic Transition

(2009) Joost W. Gouw et al.   MOLECULAR & CELLULAR 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

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

The role of oxygen availability in embryonic development and stem cell function

(2008) M. Celeste Simon et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY