Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology

Cryo-EM in molecular and cellular biology

(2022) Helen R. Saibil   MOLECULAR CELL

A ‘Build and Retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins

(2021) Chih-Chia Su et al.   NATURE METHODS

DNA origami signposts for identifying proteins on cell membranes by electron cryotomography

(2021) Emma Silvester et al.   CELL

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

(2021) Dimitry Tegunov et al.   NATURE METHODS

Current data processing strategies for cryo-electron tomography and subtomogram averaging

(2021) Euan Pyle et al.   BIOCHEMICAL JOURNAL

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

(2021) Edward L. Huttlin et al.   CELL

A streamlined workflow for automated cryo focused ion beam milling

(2021) Sebastian Tacke et al.   JOURNAL OF STRUCTURAL BIOLOGY

Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition

(2021) Jie Yu et al.   NATURE

Integrative analysis reveals unique structural and functional features of the Smc5/6 complex

(2021) You Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

(2021) Jonathan Bouvette et al.   Nature Communications

Characterization of Classical Vaccines by Charge Detection Mass Spectrometry

(2021) Lohra M. Miller et al.   ANALYTICAL CHEMISTRY

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

(2021) Tilak Kumar Gupta et al.   CELL

High-Resolution Native Mass Spectrometry

(2021) Sem Tamara et al.   CHEMICAL REVIEWS

Protein–Small Molecule Interactions in Native Mass Spectrometry

(2021) Jack L. Bennett et al.   CHEMICAL REVIEWS

Integration of Mass Spectrometry Data for Structural Biology

(2021) Hannah M. Britt et al.   CHEMICAL REVIEWS

Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding

(2021) Michael Taschner et al.   EMBO JOURNAL

Complexome Profiling: Assembly and Remodeling of Protein Complexes

(2021) Ilka Wittig et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Towards Visual Proteomics at High Resolution

(2021) Felix J.B. Bäuerlein et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of the Arabidopsis thaliana glutamate receptor-like channel GLR3.4

(2021) Marriah N. Green et al.   MOLECULAR CELL

Extracellular crosslinking mass spectrometry reveals HLA class I – HLA class II interactions on the cell surface

(2021) Gad Armony et al.   MOLECULAR IMMUNOLOGY

Structural basis of omega-3 fatty acid transport across the blood–brain barrier

(2021) Rosemary J. Cater et al.   NATURE

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain

(2021) Johannes F. Hevler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2

(2021) Moriya Slavin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition

(2021) Chi-Min Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Molecular-scale visualization of sarcomere contraction within native cardiomyocytes

(2021) Laura Burbaum et al.   Nature Communications

Reliable identification of protein-protein interactions by crosslinking mass spectrometry

(2021) Swantje Lenz et al.   Nature Communications

Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry

(2021) Sven H. Giese et al.   Nature Communications

In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli

(2021) Philipp S. Erdmann et al.   Nature Communications

A flexible framework for multi-particle refinement in cryo-electron tomography

(2021) Alister Burt et al.   PLOS BIOLOGY

Structure of the merozoite surface protein 1 from Plasmodium falciparum

(2021) Patricia M. Dijkman et al.   Science Advances

New tools for automated cryo-EM single-particle analysis in RELION-4.0

(2021) Dari Kimanius et al.   BIOCHEMICAL JOURNAL

Computed structures of core eukaryotic protein complexes

(2021) Ian R. Humphreys et al.   SCIENCE

Posttranslational Modifications Mediate the Structural Diversity of Tauopathy Strains

(2020) Tamta Arakhamia et al.   CELL

Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria–human protein interactions

(2020) Sounak Chowdhury et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

Structure of the neurotensin receptor 1 in complex with β-arrestin 1

(2020) Weijiao Huang et al.   NATURE

Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms

(2020) Antonio Martinez-Sanchez et al.   NATURE METHODS

MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells

(2020) Klaus C. Gwosch et al.   NATURE METHODS

Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry

(2020) Zachary L. VanAernum et al.   Nature Protocols

Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling

(2020) Oleg Klykov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amyloid structure determination in RELION-3.1

(2020) Sjors H. W. Scheres   Acta Crystallographica Section D-Structural Biology

Structure of RyR1 in native membranes

(2020) Wenbo Chen et al.   EMBO REPORTS

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

(2020) Chen Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Novel Applications of FIB-SEM-Based ToF-SIMS in Atom Probe Tomography Workflows

(2020) William D.A. Rickard et al.   MICROSCOPY AND MICROANALYSIS

Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins

(2020) Joseph Gault et al.   NATURE METHODS

How paired PSII–LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry

(2020) Pascal Albanese et al.   Nature Communications

The In Situ Structure of Parkinson’s Disease-Linked LRRK2

(2020) Reika Watanabe et al.   CELL

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry

(2020) Babara Steigenberger et al.   MOLECULAR & CELLULAR PROTEOMICS

Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism

(2020) Byung-Gil Lee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

In-cell architecture of an actively transcribing-translating expressome

(2020) Francis J. O’Reilly et al.   SCIENCE

Mass Spectrometry Analysis of Intact Proteins from Crude Samples

(2020) Shay Vimer et al.   ANALYTICAL CHEMISTRY

Present and Emerging Methodologies in Cryo-EM Single-Particle Analysis

(2020) Mengyu Wu et al.   BIOPHYSICAL JOURNAL

The promise and the challenges of cryo‐electron tomography

(2020) Martin Turk et al.   FEBS LETTERS

Single-particle cryo-EM at atomic resolution

(2020) Takanori Nakane et al.   NATURE

Atomic-resolution protein structure determination by cryo-EM

(2020) Ka Man Yip et al.   NATURE

Structures and distributions of SARS-CoV-2 spike proteins on intact virions

(2020) Zunlong Ke et al.   NATURE

Cryo-EM structure of coronavirus-HKU1 haemagglutinin esterase reveals architectural changes arising from prolonged circulation in humans

(2020) Daniel L. Hurdiss et al.   Nature Communications

Topaz-Denoise: general deep denoising models for cryoEM and cryoET

(2020) Tristan Bepler et al.   Nature Communications

Anatomy of a crosslinker

(2020) Adam Belsom et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM

(2020) Paul Dominic B. Olinares et al.   STRUCTURE

Rapid determination of quaternary protein structures in complex biological samples

(2019) Simon Hauri et al.   Nature Communications

A folded conformation of MukBEF and cohesin

(2019) Frank Bürmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents

(2019) Christian E. Stieger et al.   JOURNAL OF PROTEOME RESEARCH

Direct Mass Spectrometry Analysis of Protein Complexes and Intact Proteins up to >70 kDa from Tissue

(2019) Rian L. Griffiths et al.   ANALYTICAL CHEMISTRY

Membrane Protein–Lipid Interactions Probed Using Mass Spectrometry

(2019) Jani Reddy Bolla et al.   Annual Review of Biochemistry

Visualization of clustered protocadherin neuronal self-recognition complexes

(2019) Julia Brasch et al.   NATURE

eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response

(2019) Lillian R. Kenner et al.   SCIENCE

Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR

(2019) Nancy L Meyer et al.   eLife

A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue

(2019) Miroslava Schaffer et al.   NATURE METHODS

On-line protein digestion by immobilized enzyme microreactor capillary electrophoresis-mass spectrometry

(2019) Lorena Villegas et al.   TALANTA

Laser phase plate for transmission electron microscopy

(2019) Osip Schwartz et al.   NATURE METHODS

PhoX: An IMAC-Enrichable Cross-Linking Reagent

(2019) Barbara Steigenberger et al.   ACS Central Science

Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome

(2019) Kaige Yan et al.   NATURE

Structure of the Fanconi anaemia monoubiquitin ligase complex

(2019) Shabih Shakeel et al.   NATURE

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

A complete data processing workflow for cryo-ET and subtomogram averaging

(2019) Muyuan Chen et al.   NATURE METHODS

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

(2019) Chi-Min Ho et al.   NATURE METHODS

A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins

(2019) Jani Reddy Bolla et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Direct visualization of degradation microcompartments at the ER membrane

(2019) Sahradha Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-density chemical cross-linking for modeling protein interactions

(2019) Julian Mintseris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment

(2018) Qiang Guo et al.   CELL

Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei

(2018) Domenico Fasci et al.   MOLECULAR & CELLULAR PROTEOMICS

Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry

(2018) Joshua Matthew Allen Bullock et al.   STRUCTURE

An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations

(2018) Xiaonan Liu et al.   Nature Communications

Classification of Single Particles from Human Cell Extract Reveals Distinct Structures

(2018) Eric J. Verbeke et al.   Cell Reports

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue

(2018) Juan D. Chavez et al.   Cell Systems

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging

(2018) Benjamin A. Himes et al.   NATURE METHODS

A call for public archives for biological image data

(2018) Jan Ellenberg et al.   NATURE METHODS

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

(2018) Oleg Klykov et al.   Nature Protocols

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology

(2018) Francis J. O’Reilly et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry

(2018) Dror S. Chorev et al.   SCIENCE

Capturing protein communities by structural proteomics in a thermophilic eukaryote

(2017) Panagiotis L Kastritis et al.   Molecular Systems Biology

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells

(2017) Yi Yang et al.   Nature Protocols

Mechanistic insight into the assembly of the HerA–NurA helicase–nuclease DNA end resection complex

(2017) Zainab Ahdash et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry

(2017) Devin K. Schweppe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state

(2017) Joost Snijder et al.   SCIENCE

Single-protein detection in crowded molecular environments in cryo-EM images

(2017) J Peter Rickgauer et al.   eLife

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

(2016) Devin K. Schweppe et al.   BIOINFORMATICS

The diverse and expanding role of mass spectrometry in structural and molecular biology

(2016) Philip Lössl et al.   EMBO JOURNAL

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers

(2016) Xuefei Zhong et al.   JOURNAL OF PROTEOME RESEARCH

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

(2016) Florian K. M. Schur et al.   SCIENCE

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Cryo-EM single particle analysis with the Volta phase plate

(2016) Radostin Danev et al.   eLife

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

(2015) Adam Belsom et al.   MOLECULAR & CELLULAR PROTEOMICS

A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day

(2015) Fabian Hosp et al.   MOLECULAR & CELLULAR PROTEOMICS

Reproducible quantitative proteotype data matrices for systems biology

(2015) Hannes L. Röst et al.   MOLECULAR BIOLOGY OF THE CELL

Structural analysis of multicellular organisms with cryo-electron tomography

(2015) Jan Harapin et al.   NATURE METHODS

Principles of cryo-EM single-particle image processing

(2015) Fred J. Sigworth   Microscopy

Mass-Selective Soft-Landing of Protein Assemblies with Controlled Landing Energies

(2014) Victor A. Mikhailov et al.   ANALYTICAL CHEMISTRY

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

Identification of Protein Interactions Involved in Cellular Signaling

(2013) Jukka Westermarck et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

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

EMDataBank.org: unified data resource for CryoEM

(2010) C. L. Lawson et al.   NUCLEIC ACIDS RESEARCH

Visual proteomics of the human pathogen Leptospira interrogans

(2009) Martin Beck et al.   NATURE METHODS

Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions

(2008) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS