xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

The Structural Basis of Substrate Recognition by the Eukaryotic Chaperonin TRiC/CCT

(2014) Lukasz A. Joachimiak et al.   CELL

Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics

(2014) Umut H. Toprak et al.   MOLECULAR & CELLULAR PROTEOMICS

A mass spectrometry–based hybrid method for structural modeling of protein complexes

(2014) Argyris Politis et al.   NATURE METHODS

A comparative cross-linking strategy to probe conformational changes in protein complexes

(2014) Carla Schmidt et al.   Nature Protocols

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

(2014) Alexander Leitner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Subunit Topology of the INO80 Chromatin Remodeler and Its Nucleosome Complex

(2013) Alessandro Tosi et al.   CELL

Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold

(2013) Khanh Huy Bui et al.   CELL

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

(2013) Lutz Fischer et al.   Journal of Proteomics

Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification

(2013) Michael J. Trnka et al.   MOLECULAR & CELLULAR PROTEOMICS

Architecture of the large subunit of the mammalian mitochondrial ribosome

(2013) Basil J. Greber et al.   NATURE

Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline

(2013) Alexander Leitner et al.   Nature Protocols

Cross-Link Guided Molecular Modeling with ROSETTA

(2013) Abdullah Kahraman et al.   PLoS One

Comparative cross-linking and mass spectrometry of an intact F-type ATPase suggest a role for phosphorylation

(2013) Carla Schmidt et al.   Nature Communications

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

(2012) Salvatore Cappadona et al.   AMINO ACIDS

Crystal Structure of Firefly Luciferase in a Second Catalytic Conformation Supports a Domain Alternation Mechanism

(2012) Jesse A. Sundlov et al.   BIOCHEMISTRY

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

(2012) Thomas Walzthoeni et al.   NATURE METHODS

Identification of cross-linked peptides from complex samples

(2012) Bing Yang et al.   NATURE METHODS

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

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT

(2012) Alexander Leitner et al.   STRUCTURE

A Gradient of ATP Affinities Generates an Asymmetric Power Stroke Driving the Chaperonin TRIC/CCT Folding Cycle

(2012) Stefanie Reissmann et al.   Cell Reports

Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links

(2011) S. L. N. Mayne et al.   BRIEFINGS IN BIOINFORMATICS

Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle

(2011) Yao Cong et al.   EMBO JOURNAL

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

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

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

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

How does multiple testing correction work?

(2009) William S Noble   NATURE BIOTECHNOLOGY

Chaperonins: The hunt for the Group II mechanism

(2008) Maria Giulia Bigotti et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

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

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

(2008) Oliver Rinner et al.   NATURE METHODS