Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry
Open accessAbstract
Histone proteins are key components of chromatin. Their N-terminal tails are enriched in combinatorial post-translational modifications (PTMs), which influence gene regulation, DNA repair, and chromosome condensation. Mass spectrometry (MS)-based middle-down proteomics has emerged as a technique to analyze co-occurring PTMs, as it allows for the characterization of intact histone tails (>50 aa) rather than short (<20 aa) peptides analyzed by bottom-up. However, a demonstration of its reliability is still lacking. We compared results obtained with the middle-down and the bottom-up strategy in calculating PTM relative abundance and stoichiometry. Since bottom-up was proven to have biases in peptide signal detection such as uneven ionization efficiency, we performed an external correction using a synthetic peptide library with known peptide relative abundance. Corrected bottom-up data were used as reference. Calculated abundances of single PTMs showed similar deviations from the reference when comparing middle-down and uncorrected bottom-up results. Moreover, we show that the two strategies provided similar performance in defining accurate PTM stoichiometry. Collectively, we evidenced that the middle-down strategy is at least equally reliable to bottom-up in quantifying histone PTMs.
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It has been estimated that about 1,000 H3 proteoforms above a 0.1% abundance threshold exist for each of three histone H3 genes.
“It has been estimated that ~1,000 H3 proteoforms above a 0.1% abundance threshold exist for each of three histone H3 genes 50 .”
From How many human proteoforms are there? (2018) · cites this paper as [50]
The paper reports 287 nonredundant combinatorial PTMs in its middle-down analysis, but does not estimate the number of H3 proteoforms per gene. Searches for ~1,000 proteoforms, a 0.1% abundance threshold, and three H3 genes found no passage addressing that estimate. (LLM, conf=0.75)
Experimental — accuracy not yet measuredRecent estimates from middle-down studies suggest that ~1,000 proteoforms exist for each of the H3 genes.
“Recent estimates from middle-down studies suggest that ~1,000 proteoforms exist for each of the H3 genes 50,92 .”
From How many human proteoforms are there? (2018) · cites this paper as [50]
The middle-down results (page not available in our copy) report 287 nonredundant combinatorial PTMs, but give no estimate of approximately 1,000 proteoforms for each H3 gene. Searches for that estimate and for H3-gene-specific counts found no supporting passage. (LLM, conf=0.73)
Experimental — accuracy not yet measured
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- Authors
- Sidoli, S., Lin, S., Karch, K. R., & Garcia, B. A.
- Affiliations
- University of Pennsylvania (US)
- Corresponding author
- Garcia, Benjamin A.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-03-03
- Volume
- 87
- Issue
- 6
- Pages
- 3129-3133
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC4469134
- OpenAlex
- W17489521
- Cited by
- 67
- References
- 16
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 12 · 2023: 2 · 2022: 3 · 2021: 6 · 2020: 4 · 2019: 4 · 2018: 4 · 2017: 7 · 2016: 9 · 2015: 8
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH Office of the Director (DP2OD007447)
- National Institute of General Medical Sciences (R01GM11017)
- 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 › Genomics and Chromatin Dynamics
- Keywords
- histone modifications, middle-down proteomics, shotgun proteomics, histone N-terminal tails, synthetic peptide libraries, method comparison
- MeSH terms
- Chromatography, Liquid, HeLa Cells, Humans, Protein Processing, Post-Translational, Proteomics, Tandem Mass Spectrometry
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