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

Identification of Core Components and Transient Interactors of the Peroxisomal Importomer by Dual-Track Stable Isotope Labeling with Amino Acids in Cell Culture Analysis

(2012) Silke Oeljeklaus et al.   JOURNAL OF PROTEOME RESEARCH

SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments

(2012) Hyungwon Choi 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

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Dual Role of Mitofilin in Mitochondrial Membrane Organization and Protein Biogenesis

(2011) Karina von der Malsburg et al.   DEVELOPMENTAL CELL

Mapping a Dynamic Innate Immunity Protein Interaction Network Regulating Type I Interferon Production

(2011) Shitao Li et al.   IMMUNITY

CCM3/PDCD10 Heterodimerizes with Germinal Center Kinase III (GCKIII) Proteins Using a Mechanism Analogous to CCM3 Homodimerization

(2011) Derek F. Ceccarelli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure-Function Analysis of Core STRIPAK Proteins

(2011) Michelle J. Kean et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Composition and Topology of the Endoplasmic Reticulum–Mitochondria Encounter Structure

(2011) David A. Stroud et al.   JOURNAL OF MOLECULAR BIOLOGY

Joining Forces: Integrating Proteomics and Cross-linking with the Mass Spectrometry of Intact Complexes

(2011) Florian Stengel et al.   MOLECULAR & CELLULAR PROTEOMICS

MINOS1 is a conserved component of mitofilin complexes and required for mitochondrial function and cristae organization

(2011) Alwaleed K. Alkhaja et al.   MOLECULAR BIOLOGY OF THE CELL

Dual Function of Sdh3 in the Respiratory Chain and TIM22 Protein Translocase of the Mitochondrial Inner Membrane

(2011) Natalia Gebert et al.   MOLECULAR CELL

Toward an understanding of the protein interaction network of the human liver

(2011) J. Wang et al.   Molecular Systems Biology

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

(2011) K. K. Lee et al.   Molecular Systems Biology

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

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

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Defining human ERAD networks through an integrative mapping strategy

(2011) John C. Christianson et al.   NATURE CELL BIOLOGY

A roadmap to generate renewable protein binders to the human proteome

(2011) Karen Colwill et al.   NATURE METHODS

A public genome-scale lentiviral expression library of human ORFs

(2011) Xiaoping Yang et al.   NATURE METHODS

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

(2011) Dana V. Skarra et al.   PROTEOMICS

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Proteomic and Functional Genomic Landscape of Receptor Tyrosine Kinase and Ras to Extracellular Signal-Regulated Kinase Signaling

(2011) A. A. Friedman et al.   Science Signaling

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

(2010) Andrea Sinz   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

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

Modeling Contaminants in AP-MS/MS Experiments

(2010) Mathieu Lavallée-Adam et al.   JOURNAL OF PROTEOME RESEARCH

The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes

(2010) Juri Rappsilber   JOURNAL OF STRUCTURAL BIOLOGY

Crosslinking combined with mass spectrometry for structural proteomics

(2010) Evgeniy V. Petrotchenko et al.   MASS SPECTROMETRY REVIEWS

Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

(2010) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2010) Robyn M. Kaake et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted proteomics by selected reaction monitoring mass spectrometry: applications to systems biology and biomarker discovery

(2010) Sarah Elschenbroich et al.   Molecular BioSystems

Defining the budding yeast chromatin-associated interactome

(2010) Jean-Philippe Lambert et al.   Molecular Systems Biology

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

(2010) Jelle Van Leene et al.   Molecular Systems Biology

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

Native GABAB receptors are heteromultimers with a family of auxiliary subunits

(2010) Jochen Schwenk et al.   NATURE

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Quantitative proteomics of the Cav2 channel nano-environments in the mammalian brain

(2010) C. S. Muller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

(2010) J. R. A. Hutchins et al.   SCIENCE

Functional protein microarray technology

(2010) Shaohui Hu et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Literature curation of protein interactions: measuring agreement across major public databases

(2010) A. L. Turinsky et al.   Database-The Journal of Biological Databases and Curation

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

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

(2009) Silke Oeljeklaus et al.   FEBS LETTERS

The completion of the Mammalian Gene Collection (MGC)

(2009) et al.   GENOME RESEARCH

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

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

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

(2009) Timo Glatter 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

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

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

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

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors

(2009) J. Schwenk et al.   SCIENCE

PP4R4/KIAA1622 Forms a Novel Stable Cytosolic Complex with Phosphoprotein Phosphatase 4

(2008) Ginny I. Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Novel Proteomics Approach for the Discovery of Chromatin-associated Protein Networks

(2008) Jean-Philippe Lambert et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

(2008) Hyungwon Choi et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Protein production and purification

(2008) Susanne Gräslund et al.   NATURE METHODS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

A Biomedically Enriched Collection of 7000 Human ORF Clones

(2008) Andreas Rolfs et al.   PLoS One

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

Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3

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

Automated production of recombinant human proteins as resource for proteome research

(2008) Thorsten Kohl et al.   Proteome Science

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE