Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

(2013) Markku Varjosalo et al.   NATURE METHODS

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Quantitative measurements ofN-linked glycoproteins in human plasma by SWATH-MS

(2013) Yansheng Liu et al.   PROTEOMICS

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Secretomic Analysis Identifies Alpha-1 Antitrypsin (A1AT) as a Required Protein in Cancer Cell Migration, Invasion, and Pericellular Fibronectin Assembly for Facilitating Lung Colonization of Lung Adenocarcinoma Cells

(2012) Ying-Hua Chang 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

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Targeted proteomics

(2012) Vivien Marx   NATURE METHODS

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

(2012) Claudia Escher et al.   PROTEOMICS

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry

(2011) Christina Ludwig et al.   MOLECULAR & CELLULAR PROTEOMICS

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Visualization and Biochemical Analyses of the Emerging Mammalian 14-3-3-Phosphoproteome

(2011) Catherine Johnson et al.   MOLECULAR & CELLULAR PROTEOMICS

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

(2011) T. Glatter et al.   Molecular Systems Biology

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

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

(2011) Lukas Reiter et al.   NATURE METHODS

Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information

(2011) M. C. Good et al.   SCIENCE

The capture of phosphoproteins by 14-3-3 proteins mediates actions of insulin

(2011) Shuai Chen et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Dynamics of Cullin-RING Ubiquitin Ligase Network Revealed by Systematic Quantitative Proteomics

(2010) Eric J. Bennett et al.   CELL

Recent advances in charting protein–protein interaction: mass spectrometry-based approaches

(2010) Anne-Claude Gavin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Global Phosphoproteomics Identifies a Major Role for AKT and 14-3-3 in Regulating EDC3

(2010) Mark Larance et al.   MOLECULAR & CELLULAR PROTEOMICS

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

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

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

mTOR signaling at a glance

(2009) M. Laplante et al.   JOURNAL OF CELL SCIENCE

Differential 14-3-3 Affinity Capture Reveals New Downstream Targets of Phosphatidylinositol 3-Kinase Signaling

(2009) Fanny Dubois et al.   MOLECULAR & CELLULAR PROTEOMICS

Characterization of Rictor Phosphorylation Sites Reveals Direct Regulation of mTOR Complex 2 by S6K1

(2009) C. C. Dibble et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

(2009) Timo Glatter et al.   Molecular Systems Biology

Cell fate decisions are specified by the dynamic ERK interactome

(2009) Alex von Kriegsheim et al.   NATURE CELL BIOLOGY

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

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

(2009) Da Wei Huang et al.   Nature Protocols

Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells

(2009) Yu-Fei He et al.   PROTEOMICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Integrated network analysis platform for protein-protein interactions

(2008) Jianmin Wu et al.   NATURE METHODS

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

(2008) Judit Villén et al.   Nature Protocols