Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

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

(2013) Yansheng Liu et al.   PROTEOMICS

Quantitative Analysis of Hsp90-Client Interactions Reveals Principles of Substrate Recognition

(2012) Mikko Taipale et al.   CELL

Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions

(2012) Anne-Claude Gingras et al.   FEBS LETTERS

Label-free quantitative proteomics trends for protein–protein interactions

(2012) Stephen Tate et al.   Journal of Proteomics

Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins

(2012) Michelle J. Kean et al.   METHODS

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

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)

(2011) Genna L. Andrews et al.   ANALYTICAL CHEMISTRY

BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc

(2011) Jake E. Delmore et al.   CELL

Disease mutations in disordered regions—exception to the rule?

(2011) Vladimir Vacic et al.   Molecular BioSystems

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

A cost-benefit analysis of multidimensional fractionation of affinity purification-mass spectrometry samples

(2011) Wade H. Dunham et al.   PROTEOMICS

ProHits: integrated software for mass spectrometry–based interaction proteomics

(2010) Guomin Liu et al.   NATURE BIOTECHNOLOGY

HSP90 at the hub of protein homeostasis: emerging mechanistic insights

(2010) Mikko Taipale et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Strategies for Stalling Malignancy: Targeting Cancers Addiction to Hsp90

(2009) Chrisostomos Prodromou   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

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

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Kinase mutations in human disease: interpreting genotype–phenotype relationships

(2009) Piya Lahiry et al.   NATURE REVIEWS GENETICS

Protein interactions in human genetic diseases

(2008) Benjamin Schuster-Böckler et al.   GENOME BIOLOGY

4,5-Diarylisoxazole Hsp90 Chaperone Inhibitors: Potential Therapeutic Agents for the Treatment of Cancer

(2007) Paul A. Brough et al.   JOURNAL OF MEDICINAL CHEMISTRY