Profiling of Protein Interaction Networks of Protein Complexes Using Affinity Purification and Quantitative Mass Spectrometry

Investigation of protein–protein interactions in living cells by chemical crosslinking and mass spectrometry

(2010) Andrea Sinz   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

The RNA Polymerase I Transcription Machinery: An Emerging Target for the Treatment of Cancer

(2010) Denis Drygin et al.   Annual Review of Pharmacology and Toxicology

Structure and function of the GINS complex, a key component of the eukaryotic replisome

(2010) Stuart A. MacNeill   BIOCHEMICAL JOURNAL

Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery

(2010) Grzegorz M. Popowicz et al.   CELL CYCLE

Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry

(2010) Zhuo Angel Chen et al.   EMBO JOURNAL

Systematic Mutational Analysis of Peptide Inhibition of the p53–MDM2/MDMX Interactions

(2010) Chong Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Characterization of Cell Cycle Specific Protein Interaction Networks of the Yeast 26S Proteasome Complex by the QTAX Strategy

(2010) Robyn M. Kaake et al.   JOURNAL OF PROTEOME RESEARCH

Revealing Novel Telomere Proteins Usingin VivoCross-linking, Tandem Affinity Purification, and Label-free Quantitative LC-FTICR-MS

(2010) Thalia Nittis et al.   MOLECULAR & CELLULAR PROTEOMICS

Enriching quantitative proteomics with SIN

(2010) Mihaela E Sardiu et al.   NATURE BIOTECHNOLOGY

Streamlined analysis schema for high-throughput identification of endogenous protein complexes

(2010) A. Malovannaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational protein profile similarity screening for quantitative mass spectrometry experiments

(2009) Marc Kirchner et al.   BIOINFORMATICS

How and when should interactome-derived clusters be used to predict functional modules and protein function?

(2009) Jimin Song et al.   BIOINFORMATICS

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation

(2009) Ping Xu et al.   CELL

New dimensions in the study of protein complexes using quantitative mass spectrometry

(2009) Silke Oeljeklaus et al.   FEBS LETTERS

The 26 S Proteasome: From Basic Mechanisms to Drug Targeting

(2009) Ami Navon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Method for Investigating Protein−Protein Interactions Related toSalmonellaTyphimurium Pathogenesis

(2009) Saiful M. Chowdhury et al.   JOURNAL OF PROTEOME RESEARCH

Streamline Proteomic Approach for Characterizing Protein−Protein Interaction Network in a RAD52 Protein Complex

(2009) Yuchun Du et al.   JOURNAL OF PROTEOME RESEARCH

Evaluation of Clustering Algorithms for Protein Complex and Protein Interaction Network Assembly

(2009) Mihaela E. Sardiu et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Proteomics by Metabolic Labeling of Model Organisms

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

Affinity Purification Strategy to Capture Human Endogenous Proteasome Complexes Diversity and to Identify Proteasome-interacting Proteins

(2009) Marie-Pierre Bousquet-Dubouch et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Proteomics Reveals a Dynamic Interactome and Phase-Specific Phosphorylation in the Neurospora Circadian Clock

(2009) Christopher L. Baker et al.   MOLECULAR CELL

The eIF3 Interactome Reveals the Translasome, a Supercomplex Linking Protein Synthesis and Degradation Machineries

(2009) Zhe Sha et al.   MOLECULAR CELL

What recent ribosome structures have revealed about the mechanism of translation

(2009) T. Martin Schmeing et al.   NATURE

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

(2009) Noelle M Griffin et al.   NATURE BIOTECHNOLOGY

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

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

The emerging role of APC/CCdh1 in controlling differentiation, genomic stability and tumor suppression

(2009) R Wäsch et al.   ONCOGENE

Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics

(2009) Mihaela E. Sardiu et al.   PLoS One

Charting the molecular network of the drug target Bcr-Abl

(2009) M. Brehme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle

(2009) WWM Pim Pijnappel et al.   Proteome Science

Quantitative proteomics in biological research

(2009) Matthias Wilm   PROTEOMICS

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

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

(2009) Gozde Kar et al.   PLoS Computational Biology

DAnTE: a statistical tool for quantitative analysis of -omics data

(2008) A. D. Polpitiya et al.   BIOINFORMATICS

Targeting the MDM2-p53 Interaction for Cancer Therapy

(2008) S. Shangary et al.   CLINICAL CANCER RESEARCH

High confidence determination of specific protein–protein interactions using quantitative mass spectrometry

(2008) Michiel Vermeulen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Interaction networks for systems biology

(2008) Samuel Bader et al.   FEBS LETTERS

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

(2008) Laura Trinkle-Mulcahy et al.   JOURNAL OF CELL BIOLOGY

Utility of formaldehyde cross-linking and mass spectrometry in the study of protein–protein interactions

(2008) Brent W. Sutherland et al.   JOURNAL OF MASS SPECTROMETRY

Mapping the Integrin-Linked Kinase Interactome Using SILAC

(2008) Iveta Dobreva et al.   JOURNAL OF PROTEOME RESEARCH

Characterization of the Human COP9 Signalosome Complex Using Affinity Purification and Mass Spectrometry

(2008) Lei Fang et al.   JOURNAL OF PROTEOME RESEARCH

A PP2A Phosphatase High Density Interaction Network Identifies a Novel Striatin-interacting Phosphatase and Kinase Complex Linked to the Cerebral Cavernous Malformation 3 (CCM3) Protein

(2008) Marilyn Goudreault et al.   MOLECULAR & CELLULAR PROTEOMICS

Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction

(2008) Patrick Schreiner et al.   NATURE

Integrated network analysis platform for protein-protein interactions

(2008) Jianmin Wu et al.   NATURE METHODS

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis

(2008) C. Guerrero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

(2008) M. E. Sardiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics

(2008) Keiji Kito et al.   PROTEOMICS