Recent methodological advances towards single-cell proteomics

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

(2023) Laurent Gatto et al.   NATURE METHODS

Sampling the proteome by emerging single-molecule and mass spectrometry methods

(2023) Michael J. MacCoss et al.   NATURE METHODS

High sensitivity top–down proteomics captures single muscle cell heterogeneity in large proteoforms

(2023) Jake A. Melby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells

(2023) Fabian Klein et al.   Nature Communications

Counting protein molecules for single-cell proteomics

(2022) Nikolai Slavov   CELL

Nanopore-Based Protein Identification

(2022) Mazdak Afshar Bakshloo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2022) Oleg Klykov et al.   MOLECULAR CELL

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

(2022) Sofani Tafesse Gebreyesus et al.   Nature Communications

Computer-aided design of reversible hybridization chain reaction (CAD-HCR) enables multiplexed single-cell spatial proteomics imaging

(2022) Xiaohao Liu et al.   Science Advances

Deep Visual Proteomics defines single-cell identity and heterogeneity

(2022) Andreas Mund et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility profiling by ATAC-seq

(2022) Fiorella C. Grandi et al.   Nature Protocols

OpenCell: Endogenous tagging for the cartography of human cellular organization

(2022) Nathan H. Cho et al.   SCIENCE

PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements

(2022) Junyoung Seo et al.   Nature Communications

Water Droplet-in-Oil Digestion Method for Single-Cell Proteomics

(2022) Takeshi Masuda et al.   ANALYTICAL CHEMISTRY

PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood**

(2022) Gang Huang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Increasing the throughput of sensitive proteomics by plexDIA

(2022) Jason Derks et al.   NATURE BIOTECHNOLOGY

Self-supervised deep learning encodes high-resolution features of protein subcellular localization

(2022) Hirofumi Kobayashi et al.   NATURE METHODS

Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape

(2022) Tobias Ensslen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging

(2022) Shanshan He et al.   NATURE BIOTECHNOLOGY

Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device

(2022) Brian D. Reed et al.   SCIENCE

Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry

(2022) Benjamin C. Orsburn et al.   Nature Communications

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

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

Deciphering molecular interactions by proximity labeling

(2021) Wei Qin et al.   NATURE METHODS

Highly Sensitive and Multiplexed Protein Imaging With Cleavable Fluorescent Tyramide Reveals Human Neuronal Heterogeneity

(2021) Renjie Liao et al.   Frontiers in Cell and Developmental Biology

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

(2021) Michael J. Taylor et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

(2021) Diana Mahdessian et al.   NATURE

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Diagnosis of Sepsis by AI-Aided Proteomics Using 2D Electrophoresis Images of Patient Serum Incorporating Transfer Learning for Deep Neural Networks

(2021) Nobuhiro Hayashi et al.   Applied Sciences-Basel

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis

(2021) Xuehua Ma et al.   NATURE METHODS

The emerging landscape of single-molecule protein sequencing technologies

(2021) Javier Antonio Alfaro et al.   NATURE METHODS

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

(2021) Sarah Black et al.   Nature Protocols

Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy

(2021) Marcus A Woodworth et al.   NUCLEIC ACIDS RESEARCH

Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging

(2021) Xavier Rovira-Clavé et al.   Nature Communications

Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review

(2021) Alejandro Correa Rojo et al.   Frontiers in Physiology

A time-resolved proteomic and prognostic map of COVID-19

(2021) Vadim Demichev et al.   Cell Systems

Artificial intelligence for proteomics and biomarker discovery

(2021) Matthias Mann et al.   Cell Systems

High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning

(2021) Etienne Becht et al.   Science Advances

A combined approach for single-cell mRNA and intracellular protein expression analysis

(2021) Johan Reimegård et al.   Communications Biology

Phage-Based Profiling of Rare Single Cells Using Nanoparticle-Directed Capture

(2021) Yuan Ma et al.   ACS Nano

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

(2021) Evgenij Fiskin et al.   NATURE BIOTECHNOLOGY

Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins

(2021) Shengli Zhang et al.   Nature Chemistry

Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization

(2021) Daniel C. Castro et al.   NATURE METHODS

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

(2021) John W. Hickey et al.   NATURE METHODS

Multiplexed single-cell proteomics using SCoPE2

(2021) Aleksandra A. Petelski et al.   Nature Protocols

Single-cell nuclear architecture across cell types in the mouse brain

(2021) Yodai Takei et al.   SCIENCE

Multiple rereads of single proteins at single–amino acid resolution using nanopores

(2021) Henry Brinkerhoff et al.   SCIENCE

Protein identification by nanopore peptide profiling

(2021) Florian Leonardus Rudolfus Lucas et al.   Nature Communications

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

(2021) Jongmin Woo et al.   Nature Communications

Evaluation of FRET X for single-molecule protein fingerprinting

(2021) Carlos Victor de Lannoy et al.   iScience

ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes

(2021) Jessica M. Hong et al.   iScience

In silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection

(2021) Carlos de Lannoy et al.   iScience

In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells

(2020) Kosuke Hata et al.   ANALYTICAL CHEMISTRY

Unpicking the proteome in single cells

(2020) Nikolai Slavov   SCIENCE

27-Plex Tandem Mass Tag Mass Spectrometry for Profiling Brain Proteome in Alzheimer’s Disease

(2020) Zhen Wang et al.   ANALYTICAL CHEMISTRY

Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot

(2020) Jian‐An Huang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt et al.   NATURE BIOTECHNOLOGY

Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins in biological samples

(2020) Shingo Sakamoto et al.   Science Advances

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

(2020) Christoph B. Messner et al.   Cell Systems

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

(2020) Valentina Cappelletti et al.   CELL

IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues

(2020) Andrea J. Radtke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial proteomics: a powerful discovery tool for cell biology

(2019) Emma Lundberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Improvement in Classification Performance Based on Target Vector Modification for All-Transfer Deep Learning

(2019) Yoshihide Sawada et al.   Applied Sciences-Basel

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification

(2019) Shilo Ohayon et al.   PLoS Computational Biology

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

(2019) Simon Leclerc et al.   Jove-Journal of Visualized Experiments

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

(2019) Daniel P. Donnelly et al.   NATURE METHODS

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Label-Free Detection of Post-translational Modifications with a Nanopore

(2019) Laura Restrepo-Pérez et al.   NANO LETTERS

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev 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

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

(2019) Hadjer Ouldali et al.   NATURE BIOTECHNOLOGY

Relative and Absolute Quantitation in Mass Spectrometry–Based Proteomics

(2018) J. Astor Ankney et al.   Annual Review of Analytical Chemistry

Nucleosome-level 3D organization of the genome

(2018) Masae Ohno et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Extending single molecule imaging to proteome analysis by quantitation of fluorescent labeling homogeneity in complex protein samples

(2018) Simon Leclerc et al.   BIOCONJUGATE CHEMISTRY

Single-molecule peptide fingerprinting

(2018) Jetty van Ginkel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies

(2018) Samuel B. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

(2018) Ying Zhu et al.   Nature Communications

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

Live single cell mass spectrometry reveals cancer‐specific metabolic profiles of circulating tumor cells

(2018) Yasmine Abouleila et al.   CANCER SCIENCE

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

(2018) Jagannath Swaminathan et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Quantitative proteomics: challenges and opportunities in basic and applied research

(2017) Olga T Schubert et al.   Nature Protocols

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing

(2016) Ludovic C. Gillet et al.   Annual Review of Analytical Chemistry

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action

(2016) Yuan Gao et al.   NATURE

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

(2015) Fan Liu et al.   NATURE METHODS

DIA mass spectrometry

(2015) Allison Doerr   NATURE METHODS

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

A Theoretical Justification for Single Molecule Peptide Sequencing

(2015) Jagannath Swaminathan et al.   PLoS Computational Biology

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Cancer Cell Profiling by Barcoding Allows Multiplexed Protein Analysis in Fine-Needle Aspirates

(2014) A. V. Ullal et al.   Science Translational Medicine

Protein Analysis by Shotgun/Bottom-up Proteomics

(2013) Yaoyang Zhang et al.   CHEMICAL REVIEWS

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells

(2013) Charlotte Stadler et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Photocleavable DNA Barcode–Antibody Conjugates Allow Sensitive and Multiplexed Protein Analysis in Single Cells

(2012) Sarit S. Agasti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

On the Scalability and Requirements of Whole Protein Mass Spectrometry

(2011) Philip D. Compton et al.   ANALYTICAL CHEMISTRY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood

(2011) Martin Lundberg et al.   NUCLEIC ACIDS RESEARCH

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL