Identification and Quantification of Proteoforms by Mass Spectrometry
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A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post‐translational modifications. In top‐down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top‐down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.
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Peptide-to-protein inference in bottom-up proteomics causes loss of proteoform information due to shared homologous regions and low sequence coverage.
“However, the ‘peptide-to-protein inference’ problem in bottom-up proteomics leads to a loss in proteoform information because of many homologous sequence regions are shared between different protein forms and the generally low protein sequence coverage is observed [13,14].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [14]
A major technical gap in top-down proteomics is that it cannot analyze low amounts of biological material, which restricts its use for rare cells, fine needle aspiration biopsies, and tissue substructures.
“However, many challenges remain especially when dealing with scant biological samples, such as isolated rare cells, fine needle aspiration biopsies, and tissue substructures.5,17”
From Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform (2020) · cites this paper as [5]
The custom filtering step reduced redundancy in proteoform counts that is typically caused by deisotoping errors, but it also merged proteoforms differing only slightly in mass, such as disulfide or deamidation variants, and positional isoforms likely to co-elute within 15 minutes.
“This filtering step of the TopPIC result reduced the redundancy in proteoform counts, which is typically related to deisotoping errors (i.e., masses can differ by a few Da due to mis-assigned monoisotopic peaks).5 However, this also resulted in merging the proteoforms that differ in mass only slightly (e.g., disulfide, deamidation), as well as positional isoforms, which are likely to co-elute with”
From Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform (2020) · cites this paper as [5]
Bottom-up protein analysis loses information regarding protein isoforms, PTM stoichiometry, and combinatorial PTMs.
“Information regarding protein isoforms, PTM stoichiometry, and combinatorial PTMs is, however, lost when using peptides as protein surrogates.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [12]
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Mass Spectrometry Compatible Surfactant for Optimized In-Gel Protein Digestion
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Self-citationEnhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation
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Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements
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Self-citationParallel Ion Parking of Protein Mixtures
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Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics
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Self-citationProForma: A Standard Proteoform Notation
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Self-citationIntact proteome fractionation strategies compatible with mass spectrometry
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Self-citationProteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families
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Self-citationStructure determination from single molecule X-ray scattering with three photons per image
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Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics
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Self-citationDeep and quantitative top-down proteomics in clinical and translational research
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Self-citationA Method for Label-Free, Differential Top-Down Proteomics
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Self-citationComprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics
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Self-citationTop-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains
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Self-citationDai, Y., Shortreed, M. R., Scalf, M., Frey, B. L., Cesnik, A. J., Solntsev, S. K., Schaffer, L. V., & Smith, L. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00516 · Cited by 26 · see citing works
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Self-citation
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Cited by
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Top-down proteomics: challenges, innovations, and applications in basic and clinical research
Brown, K. A., Melby, J. A., Roberts, D. S., & Ge, Y. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1855982 · Cited by 152 · see citing works
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Self-citationSystematic detection of functional proteoform groups from bottom-up proteomic datasets
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MASH Explorer: A Universal Software Environment for Top-Down Proteomics
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Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms
Schaffer, L. V., Tucholski, T., Shortreed, M. R., Ge, Y., & Smith, L. M. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02343 · Cited by 17 · see citing works
Self-citation
- Authors
- Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., Sun, L., Thomas, P. M., Tucholski, T., Wang, Z., Wu, S., Wu, Z., Yu, D., Shortreed, M. R., & Smith, L. M.
- Affiliations
- University of Wisconsin–Madison (US)
- National High Magnetic Field Laboratory (US)
- Northwestern University (US)
- Indiana University Indianapolis (US)
- Brigham Young University (US)
- Michigan State University (US)
- University of Oklahoma (US)
- Corresponding author
- Smith, Lloyd M.
- ORCID
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2019-05
- Volume
- 19
- Issue
- 10
- Pages
- e1800361-e1800361
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- PMC
- PMC6602557
- OpenAlex
- W2943223113
- Cited by
- 209
- References
- 158
- Citations by year
- 2026: 15 · 2025: 16 · 2024: 22 · 2023: 42 · 2022: 38 · 2021: 27 · 2020: 32 · 2019: 16 · 2018: 1
- FWCI
- 2.93
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- PROTEOMICS (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Purdue University Indianapolis (Indiana University) (submittedVersion)
- PMC
- Funders
- NIH Office of the Director
- National Human Genome Research Institute (5T32HG002760)
- National Institute of General Medical Sciences (P41GM108569, R01GM114292, R35GM126914, T32GM008349, T32GM008505)
- Division of Materials Research (1644779)
- National Heart, Lung, and Blood Institute
- National Institutes of Health (R01GM125991, R01GM118470, R01HL109810, R01HL096971, R01GM117058, R01GM125085, S10OD018475)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- proteoforms, top-down proteomics, post-translational modification, proteoform identification, mass spectrometry
- MeSH terms
- Amino Acids, Animals, Humans, Programming Languages, Protein Processing, Post-Translational, Software, Mass Spectrometry, Reproducibility of Results, Electrophoresis, Capillary, Computational Biology, Proteome, Proteomics
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