Recent progress in mass spectrometry-based strategies for elucidating protein–protein interactions

Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics

(2021) Mi Ke et al.   Nature Communications

Crosslinking mass spectrometry: A link between structural biology and systems biology

(2021) Xiaoting Tang et al.   PROTEIN SCIENCE

Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators

(2020) Jiefu Li et al.   CELL

Click Chemistry in Proteomic Investigations

(2020) Christopher G. Parker et al.   CELL

Combining Proximity Labeling and Cross-Linking Mass Spectrometry for Proteomic Dissection of Nuclear Envelope Interactome

(2020) Cheng-Hao Liu et al.   JOURNAL OF PROTEOME RESEARCH

To Cleave or Not To Cleave in XL-MS?

(2020) B. Steigenberger et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Identifying drug targets in tissues and whole blood with thermal-shift profiling

(2020) Jessica Perrin et al.   NATURE BIOTECHNOLOGY

Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection

(2020) Yutaka Hashimoto et al.   Nature Communications

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

Meltome atlas—thermal proteome stability across the tree of life

(2020) Anna Jarzab et al.   NATURE METHODS

Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

(2020) Isabell Bludau et al.   Nature Protocols

The Origins of Organellar Mapping by Protein Correlation profiling

(2020) Matthias Mann   PROTEOMICS

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

(2020) David E. Gordon et al.   SCIENCE

Proximity‐dependent labeling methods for proteomic profiling in living cells: An update

(2020) Justin A. Bosch et al.   Wiley Interdisciplinary Reviews-Developmental Biology

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

(2019) Lukas Minus Orre et al.   MOLECULAR CELL

Pick a Tag and Explore the Functions of Your Pet Protein

(2019) Giel Vandemoortele et al.   TRENDS IN BIOTECHNOLOGY

TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity

(2019) Yongliang Zhang et al.   Nature Communications

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

(2019) Zhen-Lin Chen et al.   Nature Communications

High throughput discovery of functional protein modifications by Hotspot Thermal Profiling

(2019) Jun X. Huang et al.   NATURE METHODS

The cysteine‐free single mutant C32S of APEX2 is a highly expressed and active fusion tag for proximity labeling applications

(2019) Meng‐Sen Huang et al.   PROTEIN SCIENCE

PhoX: An IMAC-Enrichable Cross-Linking Reagent

(2019) Barbara Steigenberger et al.   ACS Central Science

Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes

(2019) Anna L. Mallam et al.   Cell Reports

Development of a Photoactivatable Proximity Labeling Method for the Identification of Nuclear Proteins

(2019) Tomonori Tamura et al.   CHEMISTRY LETTERS

Next-generation interactomics: considerations for the use of co-elution to measure protein interaction networks

(2019) Daniela Salas et al.   MOLECULAR & CELLULAR PROTEOMICS

Pervasive Protein Thermal Stability Variation during the Cell Cycle

(2018) Isabelle Becher et al.   CELL

Discovering cellular protein-protein interactions: Technological strategies and opportunities

(2018) Kevin Titeca et al.   MASS SPECTROMETRY REVIEWS

Thermal proteome profiling in bacteria: probing protein state in vivo

(2018) André Mateus et al.   Molecular Systems Biology

RNA–protein interaction detection in living cells

(2018) Muthukumar Ramanathan et al.   NATURE METHODS

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells

(2018) Chris Soon Heng Tan et al.   SCIENCE

Expanding the genetic code to study protein-protein interactions

(2018) Kathrin Lang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Efficient proximity labeling in living cells and organisms with TurboID

(2018) Tess C Branon et al.   NATURE BIOTECHNOLOGY

A proximity-tagging system to identify membrane protein–protein interactions

(2018) Qiang Liu et al.   NATURE METHODS

Context-specific interactions in literature-curated protein interaction databases

(2018) R. Greg Stacey et al.   BMC GENOMICS

Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation

(2018) Zoran Minic et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Proteome-wide analysis of protein thermal stability in the model higher plant Arabidopsis thaliana

(2018) Jeremy D. Volkening et al.   MOLECULAR & CELLULAR PROTEOMICS

Efficient and robust proteome-wide approaches for cross-linking mass spectrometry

(2018) Oleg Klykov et al.   Nature Protocols

Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles

(2018) Anne-Claude Gingras et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity

(2017) Yonglu Che et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Hydrophobic Interaction Chromatography for Bottom-Up Proteomics Analysis of Single Proteins and Protein Complexes

(2017) Michal Rackiewicz et al.   JOURNAL OF PROTEOME RESEARCH

In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein–Protein Interactions at the Peptide Level

(2017) Luitzen de Jong et al.   JOURNAL OF PROTEOME RESEARCH

The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes

(2017) Fan Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Development of Large-scale Cross-linking Mass Spectrometry

(2017) Helena Maria Barysz et al.   MOLECULAR & CELLULAR PROTEOMICS

Interactome disassembly during apoptosis occurs independent of caspase cleavage

(2017) Nichollas E Scott et al.   Molecular Systems Biology

Mechanisms for restraining cAMP-dependent protein kinase revealed by subunit quantitation and cross-linking approaches

(2017) Ryan Walker-Gray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation

(2017) Victoria Hung et al.   eLife

Click-MS: Tagless Protein Enrichment Using Bioorthogonal Chemistry for Quantitative Proteomics

(2016) Arne H. Smits et al.   ACS Chemical Biology

Direct Proximity Tagging of Small Molecule Protein Targets Using an Engineered NEDD8 Ligase

(2016) Zachary B. Hill et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

(2016) Marco Faini et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

An improved smaller biotin ligase for BioID proximity labeling

(2016) Dae In Kim et al.   MOLECULAR BIOLOGY OF THE CELL

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

(2016) Alexander Leitner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

(2016) Dan Tan et al.   eLife

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry

(2015) Fan Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

(2015) Fan Liu et al.   NATURE METHODS

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

(2015) Holger Franken et al.   Nature Protocols

Studying macromolecular complex stoichiometries by peptide-based mass spectrometry

(2015) Ingo Wohlgemuth et al.   PROTEOMICS

New Insights into the DT40 B Cell Receptor Cluster Using a Proteomic Proximity Labeling Assay

(2014) Xue-Wen Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Newin VivoCross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells

(2014) Robyn M. Kaake et al.   MOLECULAR & CELLULAR PROTEOMICS

Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence

(2014) Ariel Feiglin et al.   Molecular BioSystems

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

(2014) Raymond H.J. Staals et al.   MOLECULAR CELL

Directed evolution of APEX2 for electron microscopy and proximity labeling

(2014) Stephanie S Lam et al.   NATURE METHODS

The cellular thermal shift assay for evaluating drug target interactions in cells

(2014) Rozbeh Jafari 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

Probing nuclear pore complex architecture with proximity-dependent biotinylation

(2014) D. I. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances

(2014) Eric D. Merkley et al.   PROTEIN SCIENCE

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

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

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay

(2013) D. M. Molina et al.   SCIENCE

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Complexome Profiling Identifies TMEM126B as a Component of the Mitochondrial Complex I Assembly Complex

(2012) Heinrich Heide et al.   Cell Metabolism

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

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

Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy

(2012) Jeffrey D Martell et al.   NATURE BIOTECHNOLOGY

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Investigation of stable and transient protein-protein interactions: Past, present, and future

(2012) Armand G. Ngounou Wetie et al.   PROTEOMICS

Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis

(2012) Romy Fritzsche et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

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 proteomics approach to the cell-surface interactome using the enzyme-mediated activation of radical sources reaction

(2011) Songlin Jiang et al.   PROTEOMICS

Cleavable Cross-Linker for Protein Structure Analysis: Reliable Identification of Cross-Linking Products by Tandem MS

(2010) Mathias Q. Müller et al.   ANALYTICAL CHEMISTRY

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes

(2010) Athit Kao 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

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

A “Tagless” Strategy for Identification of Stable Protein Complexes Genome-wide by Multidimensional Orthogonal Chromatographic Separation and iTRAQ Reagent Tracking

(2008) Ming Dong et al.   JOURNAL OF PROTEOME RESEARCH

Determination of the molecular mass and dimensions of membrane proteins by size exclusion chromatography

(2008) Edmund R.S. Kunji et al.   METHODS

Estimating the size of the human interactome

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