ReviewNature methods2019
Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.
Abstract readReview
In one paragraph
Review in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
162citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
162 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.Nature methods · 2023Guideline
- Marigold suspension cell culture as production system for recombinant DsRed and brazzein.Plant cell reports · 2026Article
- Modulating proteoform charge states and signal intensities in LC-MS using a nanoflow sheath liquid interface.Analytical and bioanalytical chemistry · 2026Article
- A Draft Map of E. coli Proteoforms.Analytical chemistry · 2026Article
- Article
- Deep Proteoform Sequencing with Top-Down Direct Mass Technology.bioRxiv : the preprint server for biology · 2026Article
- Top-Down Mass Spectrometry and Its Current Applications in Biomarker Discovery in Aging and Age-Related Diseases.International journal of molecular sciences · 2026Review
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry.ACS central science · 2026Article
- Intact Proteoform Analysis by Capillary Electrophoresis-Mass Spectrometry. Are We There Yet?Angewandte Chemie (International ed. in English) · 2026Article
- Top-Down Proteomics: Why and When?Proteomics · 2025Article
- Comparative Analysis of Proteoform Clean-Up Methods for In-Depth Top-Down Proteomics.Proteomics · 2025Article
- Development of a Mesothelin-Binding Engineered Scaffold Protein as a Theranostic for Pleural Mesothelioma.Bioconjugate chemistry · 2025Article
- Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.Proteomics · 2025Review
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Uncovering hidden protein modifications with native top-down mass spectrometry.Nature methods · 2025Article
- Evaluation of Protein Ion Relative Ratio Quantification in Top-down Electrospray Ionization-Mass Spectrometry Using Site-Specific Acetylated Recombinant Histone H3 Proteoforms.Journal of the American Society for Mass Spectrometry · 2025Article
- Sample preparation and cleanup methods for clinical top-down proteomics.Expert review of proteomics · 2025Review
- The Potential of Nanopore Technologies in Peptide and Protein Sensing for Biomarker Detection.Biosensors · 2025Review
- Review
102 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
28 authors.
Daniel P DonnellyBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7846-322X
Catherine M RawlinsBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.
Caroline J DeHartDepartments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
Luca FornelliDepartments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
Luis F SchachnerDepartments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.ORCID http://orcid.org/0000-0001-6157-0937
Ziqing LinDepartment of Cell and Regenerative Biology, Department of Chemistry, Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA.
Jennifer L LippensAmgen Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, CA, USA.ORCID http://orcid.org/0000-0002-6805-7922
Krishna C AluriBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7460-8727
Richa SarinBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-2953-428X
Bifan ChenDepartment of Cell and Regenerative Biology, Department of Chemistry, Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA.ORCID http://orcid.org/0000-0003-0379-0821
Carter LantzDepartment of Chemistry and Biochemistry, Department of Biological Chemistry, and UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.
Wonhyeuk JungDepartment of Chemistry and Biochemistry, Department of Biological Chemistry, and UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.
Kendall R JohnsonBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.
Antonius KollerBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.
Jeremy J WolffBruker Daltonics, Billerica, MA, USA.
Iain D G CampuzanoAmgen Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, CA, USA.ORCID http://orcid.org/0000-0003-4310-8540
Jared R AuclairBiopharmaceutical Analysis Training Laboratory, Northeastern University, Burlington, MA, USA.ORCID http://orcid.org/0000-0002-3094-1544
Alexander R IvanovBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.
Julian P WhiteleggeThe Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-2763-7733
Ljiljana Paša-TolićEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0001-9853-5457
Julia Chamot-RookeMass Spectrometry for Biology Unit, Institut Pasteur, USR 2000, CNRS, Paris, France.ORCID http://orcid.org/0000-0002-9427-543X
Paul O DanisEastwoods Consulting, Boylston, MA, USA.
Lloyd M SmithDepartment of Chemistry, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
Yury O TsybinSpectroswiss, Lausanne, Switzerland.ORCID http://orcid.org/0000-0001-7533-0774
Joseph A LooDepartment of Chemistry and Biochemistry, Department of Biological Chemistry, and UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-9989-1437
Ying GeDepartment of Cell and Regenerative Biology, Department of Chemistry, Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA.ORCID http://orcid.org/0000-0001-5211-6812
Neil L KelleherDepartments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.ORCID http://orcid.org/0000-0002-8815-3372
Jeffrey N AgarBarnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA. j.agar@northeastern.edu.ORCID http://orcid.org/0000-0003-2645-1873
Funding
Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PETER J TONTONOZ · 2003 to 2026
$40.4MUCLA NIGMS T32 Program AssessmentT32GM007185 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TORRES, JORGE · 1985 to 2020
$21.7MTR&D 7: Cell Specific ProteomicsP41GM108569 · NIGMS · NORTHWESTERN UNIVERSITY · PI KELLEHER, NEIL L · 2015 to 2024
$13.6MEffect of methodological and biological variability on molecular profiling of extracellular vesicles in cancer detectionR01CA218500 · NCI · NORTHEASTERN UNIVERSITY · PI GHIRAN, IONITA CALIN, IVANOV, ALEXANDER R. · 2018 to 2022
$4.0MUV Laser for Photodissociation-Mass Spectrometry of Proteins and Protein ComplexesR01GM103479 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LOO, JOSEPH A · 2012 to 2021
$3.2MChemistry of Life Processes Predoctoral Training ProgramT32GM105538 · NIGMS · NORTHWESTERN UNIVERSITY · PI KELLEHER, NEIL L · 2013 to 2022
$2.7MUltra-High Resolution Mass Spectrometer for Biomedical ResearchS10RR028893 · NCRR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LOO, JOSEPH A · 2010 to 2010
$2.7MEnabling Top-Down Proteomics through Materials Chemistry and NanotechnologyR01GM117058 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI GE, YING, JIN, SONG · 2015 to 2023
$2.7MUltra High Resolution Mass Spectrometer for Biomedical ResearchS10OD018475 · OD · UNIVERSITY OF WISCONSIN-MADISON · PI GE, YING · 2015 to 2015
$2.0MStructural Consequences of ALS-related Modifications of SOD1R01NS065263 · NINDS · NORTHEASTERN UNIVERSITY · PI AGAR, JEFFREY NEIL · 2009 to 2013
$1.7MDeep Proteomic Profiling of Rare CellsR01GM120272 · NIGMS · NORTHEASTERN UNIVERSITY · PI IVANOV, ALEXANDER R. · 2016 to 2019
$1.5MHigh-Resolution Ion Mobility Mass SpectrometerS10OD018504 · OD · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LOO, JOSEPH A · 2014 to 2014
$915kNCI NIH HHS R01 CA218500NCRR NIH HHS S10 RR028893NIDDK NIH HHS P30 DK063491NIGMS NIH HHS P41 GM108569NIGMS NIH HHS R01 GM103479NIGMS NIH HHS R01 GM117058NIGMS NIH HHS R01 GM120272NIGMS NIH HHS T32 GM007185NIGMS NIH HHS T32 GM105538NIH HHS S10 OD018475NIH HHS S10 OD018504NINDS NIH HHS R01 NS065263
Abstract
One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass. Top-down mass spectrometry enables the analysis of intact proteins and proteoforms. Here members of the Consortium for Top-Down Proteomics provide a decision tree that guides researchers to robust protocols for mass analysis of intact proteins (antibodies, membrane proteins and others) from mixtures of varying complexity. We also present cross-platform analytical benchmarks using a protein standard sample, to allow users to gauge their proficiency.
Indexed as
BenchmarkingMass SpectrometryProtein DenaturationProtein Processing, Post-TranslationalProteinsProteomicsProteins
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.