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

Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography

(2012) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

(2012) K. Lasker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in the Mass Spectrometry of Membrane Proteins: From Individual Proteins to Intact Complexes

(2011) Nelson P. Barrera et al.   Annual Review of Biochemistry

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

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

SnapShot: Protein-Protein Interaction Networks

(2011) Jan Seebacher et al.   CELL

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

Protein-nucleic acid complexes and the role of mass spectrometry in their structure determination

(2011) Ah Young Park et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Structural analysis of vascular endothelial growth factor receptor-2/ligand complexes by small-angle X-ray solution scattering

(2011) Kaisa Kisko et al.   FASEB JOURNAL

Cross-linking Measurements ofIn VivoProtein Complex Topologies

(2011) Chunxiang Zheng et al.   MOLECULAR & CELLULAR PROTEOMICS

Insights into EB1 structure and the role of its C-terminal domain for discriminating microtubule tips from the lattice

(2011) Rubén M. Buey et al.   MOLECULAR BIOLOGY OF THE CELL

The Catalytic Activity of Ubp6 Enhances Maturation of the Proteasomal Regulatory Particle

(2011) Eri Sakata et al.   MOLECULAR CELL

Structural basis for the subunit assembly of the anaphase-promoting complex

(2011) Anne Schreiber et al.   NATURE

Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex

(2011) M. G. Gold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass Spectrometry Reveals Stable Modules in holo and apo RNA Polymerases I and III

(2011) Laura A. Lane et al.   STRUCTURE

Chemical Cross-Linking and Mass Spectrometry As a Low-Resolution Protein Structure Determination Technique

(2010) Pragya Singh et al.   ANALYTICAL CHEMISTRY

Alternate Dissociation Pathways Identified in Charge-Reduced Protein Complex Ions

(2010) Kevin Pagel et al.   ANALYTICAL CHEMISTRY

Collision Cross Sections of Proteins and Their Complexes: A Calibration Framework and Database for Gas-Phase Structural Biology

(2010) Matthew F. Bush et al.   ANALYTICAL CHEMISTRY

ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite

(2010) Evgeniy V Petrotchenko et al.   BMC 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

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

(2010) Zhuo Angel Chen et al.   EMBO JOURNAL

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

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

Database Search Algorithm for Identification of Intact Cross-Links in Proteins and Peptides Using Tandem Mass Spectrometry

(2010) Hua Xu et al.   JOURNAL OF PROTEOME RESEARCH

Detecting Cross-Linked Peptides by Searching against a Database of Cross-Linked Peptide Pairs

(2010) Sean McIlwain 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

Ion Mobility Mass Spectrometry of Two Tetrameric Membrane Protein Complexes Reveals Compact Structures and Differences in Stability and Packing

(2010) Sheila C. Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Topographic Studies of the GroEL-GroES Chaperonin Complex by Chemical Cross-linking Using Diformyl Ethynylbenzene

(2010) Michael J. Trnka 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

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

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

Structures of APC/CCdh1 with substrates identify Cdh1 and Apc10 as the D-box co-receptor

(2010) Paula C. A. da Fonseca et al.   NATURE

Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin

(2010) Inés G Muñoz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Preparation and topology of the Mediator middle module

(2010) Tobias Koschubs et al.   NUCLEIC ACIDS RESEARCH

Integrating Ion Mobility Mass Spectrometry with Molecular Modelling to Determine the Architecture of Multiprotein Complexes

(2010) Argyris Politis et al.   PLoS One

Quaternary dynamics and plasticity underlie small heat shock protein chaperone function

(2010) F. Stengel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution

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

Defining the mechanism of polymerization in the serpinopathies

(2010) U. I. Ekeowa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure, function and mechanism of the anaphase promoting complex (APC/C)

(2010) David Barford   QUARTERLY REVIEWS OF BIOPHYSICS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

A Single Subunit Directs the Assembly of the Escherichia coli DNA Sliding Clamp Loader

(2010) Ah Young Park et al.   STRUCTURE

When proteomics meets structural biology

(2010) Min Zhou et al.   TRENDS IN BIOCHEMICAL SCIENCES

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Multiple Proteasome-Interacting Proteins Assist the Assembly of the Yeast 19S Regulatory Particle

(2009) Yasushi Saeki et al.   CELL

Ion mobility mass spectrometry of proteins and proteinassemblies

(2009) Charlotte Uetrecht et al.   CHEMICAL SOCIETY REVIEWS

Chaperonin Complexes Monitored by Ion Mobility Mass Spectrometry

(2009) Esther van Duijn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Finding Chimeras: a Bioinformatics Strategy for Identification of Cross-linked Peptides

(2009) Feixia Chu et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2009) Timo Glatter et al.   Molecular Systems Biology

Chaperone-mediated pathway of proteasome regulatory particle assembly

(2009) Jeroen Roelofs et al.   NATURE

Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions

(2009) Nelson P Barrera et al.   NATURE METHODS

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

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

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

Molecular mechanisms of proteasome assembly

(2009) Shigeo Murata et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Isoforms of U1-70k Control Subunit Dynamics in the Human Spliceosomal U1 snRNP

(2009) Helena Hernández et al.   PLoS One

Structure of the Anaphase-Promoting Complex/Cyclosome Interacting with a Mitotic Checkpoint Complex

(2009) F. Herzog et al.   SCIENCE

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Symmetrical Modularity of the COP9 Signalosome Complex Suggests its Multifunctionality

(2009) Michal Sharon et al.   STRUCTURE

Subunit Architecture of Multiprotein Assemblies Determined Using Restraints from Gas-Phase Measurements

(2009) Tara L. Pukala et al.   STRUCTURE

Subunit Architecture of Intact Protein Complexes from Mass Spectrometry and Homology Modeling†

(2008) Thomas Taverner et al.   ACCOUNTS OF CHEMICAL RESEARCH

Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy

(2008) Pragya Singh et al.   ANALYTICAL CHEMISTRY

Quadrupole-Time-of-Flight Mass Spectrometer Modified for Higher-Energy Dissociation Reduces Protein Assemblies to Peptide Fragments

(2008) Justin L. P. Benesch et al.   ANALYTICAL CHEMISTRY

Implications for Kinetochore-Microtubule Attachment from the Structure of an Engineered Ndc80 Complex

(2008) Claudio Ciferri et al.   CELL

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

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

Structure of the Human 26S Proteasome

(2008) Paula C. A. da Fonseca et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Acetylation of L12 Increases Interactions in the Escherichia coli Ribosomal Stalk Complex

(2008) Yuliya Gordiyenko et al.   JOURNAL OF MOLECULAR BIOLOGY

Collisional activation of protein complexes: Picking up the pieces

(2008) Justin L. P. Benesch   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes

(2008) Young Jin Lee   Molecular BioSystems

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Erratum: Corrigendum: Identification of cross-linked peptides from large sequence databases

(2008) Oliver Rinner et al.   NATURE METHODS

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS

Native mass spectrometry: a bridge between interactomics and structural biology

(2008) Albert J R Heck   NATURE METHODS

Ion mobility–mass spectrometry analysis of large protein complexes

(2008) Brandon T Ruotolo et al.   Nature Protocols

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

High-resolution mass spectrometry of viral assemblies: Molecular composition and stability of dimorphic hepatitis B virus capsids

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

Micelles Protect Membrane Complexes from Solution to Vacuum

(2008) N. P. Barrera et al.   SCIENCE