Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments
Published 2023 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments
Authors
Keywords
-
Journal
NATURE METHODS
Volume 20, Issue 3, Pages 375-386
Publisher
Springer Science and Business Media LLC
Online
2023-03-03
DOI
10.1038/s41592-023-01785-3
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA
- (2023) Jason Derks et al. Journal of Proteome Research
- Learning from natural variation across the proteomes of single cells
- (2022) Nikolai Slavov PLOS BIOLOGY
- Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
- (2022) Deanna L. Plubell et al. JOURNAL OF PROTEOME RESEARCH
- Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics
- (2022) Benjamin Furtwängler et al. MOLECULAR & CELLULAR PROTEOMICS
- Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
- (2022) Andreas‐David Brunner et al. Molecular Systems Biology
- Deep Visual Proteomics defines single-cell identity and heterogeneity
- (2022) Andreas Mund et al. NATURE BIOTECHNOLOGY
- Microanalysis of Brain Angiotensin Peptides Using Ultrasensitive Capillary Electrophoresis Trapped Ion Mobility Mass Spectrometry
- (2022) Kellen DeLaney et al. ANALYTICAL CHEMISTRY
- Increasing the throughput of sensitive proteomics by plexDIA
- (2022) Jason Derks et al. NATURE BIOTECHNOLOGY
- On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS
- (2022) Kendall R. Johnson et al. ANALYTICAL CHEMISTRY
- Sensitive protein analysis with plexDIA
- (2022) Arunima Singh NATURE METHODS
- Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier
- (2022) Aleksandra A. Petelski et al. Jove-Journal of Visualized Experiments
- In Vivo Subcellular Mass Spectrometry Enables Proteo‐Metabolomic Single‐cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)
- (2021) Camille Lombard-Banek et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection
- (2021) William E. Fondrie et al. JOURNAL OF PROTEOME RESEARCH
- Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years
- (2021) Gilbert S. Omenn MOLECULAR & CELLULAR PROTEOMICS
- A Simple Optimization Workflow to Enable Precise and Accurate Imputation of Missing Values in Proteomic Data Sets
- (2021) Kruttika Dabke et al. JOURNAL OF PROTEOME RESEARCH
- Measuring Protein Shapes in Living Cells
- (2021) Nikolai Slavov JOURNAL OF PROTEOME RESEARCH
- Increasing proteomics throughput
- (2021) Nikolai Slavov NATURE BIOTECHNOLOGY
- Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial
- (2021) Jelena Čuklina et al. Molecular Systems Biology
- Towards resolving proteomes in single cells
- (2021) Arunima Singh NATURE METHODS
- Quantitative single-cell proteomics as a tool to characterize cellular hierarchies
- (2021) Erwin M. Schoof et al. Nature Communications
- Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry
- (2021) Sam B. Choi et al. ANALYTICAL CHEMISTRY
- Replication of single-cell proteomics data reveals important computational challenges
- (2021) Christophe Vanderaa et al. Expert Review of Proteomics
- Driving Single Cell Proteomics Forward with Innovation
- (2021) Nikolai Slavov JOURNAL OF PROTEOME RESEARCH
- Features of Peptide Fragmentation Spectra in Single-Cell Proteomics
- (2021) Hannah Boekweg et al. JOURNAL OF PROTEOME RESEARCH
- Scaling Up Single-Cell Proteomics
- (2021) Nikolai Slavov MOLECULAR & CELLULAR PROTEOMICS
- Multiplexed single-cell proteomics using SCoPE2
- (2021) Aleksandra A. Petelski et al. Nature Protocols
- The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
- (2021) Yasset Perez-Riverol et al. NUCLEIC ACIDS RESEARCH
- A proteomics sample metadata representation for multiomics integration and big data analysis
- (2021) Chengxin Dai 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
- Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry
- (2020) Yongzheng Cong et al. ANALYTICAL CHEMISTRY
- Unpicking the proteome in single cells
- (2020) Nikolai Slavov SCIENCE
- Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
- (2020) Nicholas Lytal et al. Frontiers in Genetics
- Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms
- (2020) Jean-Christophe Beltra et al. IMMUNITY
- A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics
- (2020) Lisa M. Bramer et al. JOURNAL OF PROTEOME RESEARCH
- Single-Cell Proteomics: Progress and Prospects
- (2020) Ryan T. Kelly MOLECULAR & CELLULAR PROTEOMICS
- Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling
- (2020) Yiran Liang et al. ANALYTICAL CHEMISTRY
- Defining the carrier proteome limit for single-cell proteomics
- (2020) Tommy K. Cheung et al. NATURE METHODS
- Single-cell protein analysis by mass spectrometry
- (2020) Nikolai Slavov CURRENT OPINION IN CHEMICAL BIOLOGY
- Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis
- (2019) Robert J. Chalkley et al. MOLECULAR & CELLULAR PROTEOMICS
- DO-MS: Data-Driven Optimization of Mass Spectrometry Methods
- (2019) R. Gray Huffman et al. JOURNAL OF PROTEOME RESEARCH
- Best practices and benchmarks for intact protein analysis for top-down mass spectrometry
- (2019) Daniel P. Donnelly et al. NATURE METHODS
- Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
- (2019) Wenguang Shao et al. Nature Communications
- DART-ID increases single-cell proteome coverage
- (2019) Albert Tian Chen et al. PLoS Computational Biology
- A dream of single-cell proteomics
- (2019) Vivien Marx NATURE METHODS
- Single-cell proteomics reveals changes in expression during hair-cell development
- (2019) Ying Zhu et al. eLife
- Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS
- (2018) Ying Zhu et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Transformative Opportunities for Single-Cell Proteomics
- (2018) Harrison Specht et al. JOURNAL OF PROTEOME RESEARCH
- Intelligent image-based in situ single-cell isolation
- (2018) Csilla Brasko et al. Nature Communications
- Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells
- (2018) Ying Zhu et al. Nature Communications
- What exactly is ‘N’ in cell culture and animal experiments?
- (2018) Stanley E. Lazic et al. PLOS BIOLOGY
- Single cell protein analysis for systems biology
- (2018) Ezra Levy et al. Essays in Biochemistry
- Assembling the Community-Scale Discoverable Human Proteome
- (2018) Mingxun Wang et al. Cell Systems
- Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories
- (2018) Lindsay K. Pino et al. ANALYTICAL CHEMISTRY
- Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry
- (2018) Andrew Reichard et al. CYTOMETRY PART A
- Quantifying Homologous Proteins and Proteoforms
- (2018) Dmitry Malioutov et al. MOLECULAR & CELLULAR PROTEOMICS
- The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
- (2017) Juan Antonio Vizcaíno et al. MOLECULAR & CELLULAR PROTEOMICS
- Post-transcriptional regulation across human tissues
- (2017) Alexander Franks et al. PLoS Computational Biology
- Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies
- (2016) Cosmin Lazar et al. JOURNAL OF PROTEOME RESEARCH
- A multicenter study benchmarks software tools for label-free proteome quantification
- (2016) Pedro Navarro et al. NATURE BIOTECHNOLOGY
- Ten Simple Rules for Taking Advantage of Git and GitHub
- (2016) Yasset Perez-Riverol et al. PLoS Computational Biology
- The FAIR Guiding Principles for scientific data management and stewardship
- (2016) Mark D. Wilkinson et al. Scientific Data
- An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood
- (2015) Siyang Li et al. MOLECULAR & CELLULAR PROTEOMICS
- Single-cell messenger RNA sequencing reveals rare intestinal cell types
- (2015) Dominic Grün et al. NATURE
- Mass spectrometry imaging with laser-induced postionization
- (2015) J. Soltwisch et al. SCIENCE
- The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
- (2014) Johannes Griss et al. MOLECULAR & CELLULAR PROTEOMICS
- Mass spectrometry of intact membrane protein complexes
- (2013) Arthur Laganowsky et al. Nature Protocols
- Investigation of carryover of peptides in nano-liquid chromatography/mass spectrometry using packed and monolithic capillary columns
- (2012) Sebastiaan Dolman et al. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
- mzML—a Community Standard for Mass Spectrometry Data
- (2010) Lennart Martens et al. MOLECULAR & CELLULAR PROTEOMICS
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started