A Pipeline for Determining Protein–Protein Interactions and Proximities in the Cellular Milieu

UvrD facilitates DNA repair by pulling RNA polymerase backwards

(2014) Vitaly Epshtein et al.   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Affinity Proteomics Reveals Human Host Factors Implicated in Discrete Stages of LINE-1 Retrotransposition

(2013) Martin S. Taylor et al.   CELL

Protein Analysis by Shotgun/Bottom-up Proteomics

(2013) Yaoyang Zhang et al.   CHEMICAL REVIEWS

In VivoCross-linking Reveals Principally Oligomeric Forms of α-Synuclein and β-Synuclein in Neurons and Non-neural Cells

(2013) Ulf Dettmer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy

(2013) Chad R. Weisbrod et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers

(2013) Lutz Fischer et al.   Journal of Proteomics

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

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Rif1 Prevents Resection of DNA Breaks and Promotes Immunoglobulin Class Switching

(2013) M. Di Virgilio et al.   SCIENCE

Mass Spectrometry–Based Proteomics and Network Biology

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

Exploring the Topology of the Gid Complex, the E3 Ubiquitin Ligase Involved in Catabolite-induced Degradation of Gluconeogenic Enzymes

(2012) Ruth Menssen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure–function mapping of a heptameric module in the nuclear pore complex

(2012) Javier Fernandez-Martinez et al.   JOURNAL OF CELL BIOLOGY

Mapping the Protein Interaction Network of the Human COP9 Signalosome Complex Using a Label-free QTAX Strategy

(2012) Lei Fang et al.   MOLECULAR & CELLULAR PROTEOMICS

Activation of DSB Processing Requires Phosphorylation of CtIP by ATR

(2012) Shaun E. Peterson et al.   MOLECULAR CELL

Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes

(2012) MARK C. FIELD et al.   PARASITOLOGY

Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach

(2012) Xiang Li et al.   PROTEIN SCIENCE

In vivo protein complex topologies: Sights through a cross-linking lens

(2012) James E. Bruce   PROTEOMICS

Mass Spectrometry in the Postgenomic Era

(2011) Brian T. Chait   Annual Review of Biochemistry

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

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

The structural basis for MCM2–7 helicase activation by GINS and Cdc45

(2011) Alessandro Costa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Host Factors Associated with the Sindbis Virus RNA-Dependent RNA Polymerase: Role for G3BP1 and G3BP2 in Virus Replication

(2010) I. M. Cristea et al.   JOURNAL OF VIROLOGY

Merging Molecular Electron Microscopy and Mass Spectrometry by Carbon Film-assisted Endoproteinase Digestion

(2010) Florian M. Richter et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

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

RING Domain E3 Ubiquitin Ligases

(2009) Raymond J. Deshaies et al.   Annual Review of Biochemistry

Concerted Loading of Mcm2–7 Double Hexamers around DNA during DNA Replication Origin Licensing

(2009) Dirk Remus et al.   CELL

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Rrp17p Is a Eukaryotic Exonuclease Required for 5′ End Processing of Pre-60S Ribosomal RNA

(2009) Marlene Oeffinger et al.   MOLECULAR CELL

Human Cytomegalovirus Protein UL38 Inhibits Host Cell Stress Responses by Antagonizing the Tuberous Sclerosis Protein Complex

(2008) Nathaniel J. Moorman et al.   Cell Host & Microbe

Mapping multiprotein complexes by affinity purification and mass spectrometry

(2008) Mark O Collins et al.   CURRENT OPINION IN BIOTECHNOLOGY

Contemporary strategies for the stabilization of peptides in the α-helical conformation

(2008) Laura K Henchey et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Rapid Isolation and Identification of Bacteriophage T4-Encoded Modifications ofEscherichia coliRNA Polymerase: A Generic Method to Study Bacteriophage/Host Interactions

(2008) Lars F. Westblade et al.   JOURNAL OF PROTEOME RESEARCH

In Vivo Identification of the Outer Membrane Protein OmcA−MtrC Interaction Network inShewanella oneidensisMR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers

(2008) Haizhen Zhang et al.   JOURNAL OF PROTEOME RESEARCH

The Yeast GID Complex, a Novel Ubiquitin Ligase (E3) Involved in the Regulation of Carbohydrate Metabolism

(2008) Olivier Santt et al.   MOLECULAR BIOLOGY OF THE CELL

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

(2008) Igor Ulitsky et al.   Molecular Systems Biology

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

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