Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements
Open accessAbstract
Proteomics is presently dominated by the “bottom-up” strategy, in which proteins are enzymatically digested into peptides for mass spectrometric identification. Although this approach is highly effective at identifying large numbers of proteins present in complex samples, the digestion into peptides renders it impossible to identify the proteoforms from which they were derived. We present here a powerful new strategy for the identification of proteoforms and the elucidation of proteoform families (groups of related proteoforms) from the experimental determination of the accurate proteoform mass and number of lysine residues contained. Accurate proteoform masses are determined by standard LC–MS analysis of undigested protein mixtures in an Orbitrap mass spectrometer, and the lysine count is determined using the NeuCode isotopic tagging method. We demonstrate the approach in analysis of the yeast proteome, revealing 8637 unique proteoforms and 1178 proteoform families. The elucidation of proteoforms and proteoform families afforded here provides an unprecedented new perspective upon proteome complexity and dynamics.
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Comparing experimental masses with one another revealed related proteoforms that differ by common PTMs, yielding additional identifications.
“Further comparisons of all experimental masses with one another revealed related proteoforms differing by common PTMs, yielding more identifications.”
From Proteoforms as the next proteomics currency (2018) · cites this paper as [9]
Comparing measured masses and lysine counts with a theoretical database of possible yeast proteoforms produced proteoform identifications.
“Comparison of the measured masses and lysine counts with a theoretical database of possible yeast proteoforms yielded proteoform identifications.”
From Proteoforms as the next proteomics currency (2018) · cites this paper as [9]
These pairwise relationships-experimental versus theoretical and experimental versus experimental-were assembled into families of related proteoforms.
“These pairwise relations (experimental:theoretical and experimental:experimental) were assembled into “families” of related proteoforms (see the figure, top center).”
From Proteoforms as the next proteomics currency (2018) · cites this paper as [9]
A complementary approach identified proteoforms across the yeast proteome using high-accuracy intact mass measurements aided by lysine residue counts.
“A complementary approach reported the proteome-wide identification of proteoforms in yeast, based primarily upon a high-accuracy determination of their intact mass, aided by a corollary measurement of the number of lysine residues in the molecule (9).”
From Proteoforms as the next proteomics currency (2018) · cites this paper as [9]
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Cupp‐Sutton, K. A., Atallah, M. A., Zhao, Z., Anjum, S., Chowdhury, T., Sunny, A. T., Szamweber, P., & Wu, S. (2026) · Mass Spectrometry Reviews · doi:10.1002/mas.70051
- Authors
- Shortreed, M. R., Frey, B. L., Scalf, M., Knoener, R. A., Cesnik, A. J., & Smith, L. M.
- Affiliations
- University of Wisconsin System (US)
- Corresponding author
- Smith, Lloyd M.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-03-04
- Volume
- 15
- Issue
- 4
- Pages
- 1213-1221
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC4917391
- OpenAlex
- W2289907074
- Cited by
- 58
- References
- 35
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 4 · 2023: 4 · 2022: 5 · 2021: 4 · 2020: 3 · 2019: 9 · 2018: 8 · 2017: 6 · 2016: 1
- FWCI
- 3.98
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Proteome Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM103315, R01GM114292)
- 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, Orbitrap mass spectrometry, yeast proteome, proteome complexity, top-down proteomics
- MeSH terms
- Chromatography, Liquid, Lysine, Molecular Weight, Ribosomal Proteins, Saccharomyces cerevisiae, Mass Spectrometry, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins, Proteomics, Multiprotein Complexes, Ribosome Subunits, Large, Eukaryotic
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