Evaluation of the Compact High-Field Orbitrap for Top-Down Proteomics of Human Cells
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Mass spectrometry based proteomics generally seeks to identify and fully characterize protein species with high accuracy and throughput. Recent improvements in protein separation have greatly expanded the capacity of top-down proteomics (TDP) to identify a large number of intact proteins. To date, TDP has been most tightly associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Here, we couple the improved separations to a Fourier-transform instrument based not on ICR but using the Orbitrap Elite mass analyzer. Application of this platform to H1299 human lung cancer cells resulted in the unambiguous identification of 690 unique proteins and over 2000 proteoforms identified from proteins with intact masses<50 kDa. This is an early demonstration of high throughput TDP (>500 identifications) in an Orbitrap mass spectrometer and exemplifies an accessible platform for whole protein mass spectrometry.
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Top-down proteomics is currently applied mainly to proteoforms smaller than 30 kDa, because high-resolution FTMS performs poorly for larger proteoforms and intact proteomes in the 30-60 kDa range are highly complex.
“top-down proteomics (TDP) is currently mostly applied to the characterization of proteoforms <30 kDa due to the poor performance of high-resolution FTMS for the analysis of larger proteoforms and the high complexity of intact proteomes in the 30–60 kDa mass range.”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [18]
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- Authors
- Ahlf, D. R., Compton, P. D., Tran, J. C., Early, B. P., Thomas, P. M., & Kelleher, N. L.
- Affiliations
- Northwestern University (US)
- Corresponding author
- Kelleher, Neil L.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-07-13
- Volume
- 11
- Issue
- 8
- Pages
- 4308-4314
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC3437942
- OpenAlex
- W1964946814
- Cited by
- 89
- References
- 26
- Citations by year
- 2026: 2 · 2024: 2 · 2023: 1 · 2022: 1 · 2021: 5 · 2020: 5 · 2019: 4 · 2018: 8 · 2017: 10 · 2016: 11 · 2015: 13 · 2014: 10 · 2013: 14 · 2012: 1
- FWCI
- 5.37
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation
- Chicago Community Trust
- Northwestern University
- Chicago Biomedical Consortium
- National Institutes of Health
- National Institute on Drug Abuse (DA018310, P30DA018310)
- National Institute of General Medical Sciences (R01GM067193, GM 067193)
- 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
- top-down proteomics, proteoforms, H1299 cells, high-throughput proteomics, protein mass spectrometry
- MeSH terms
- Amino Acid Sequence, Camptothecin, DNA Damage, Fourier Analysis, Humans, Molecular Sequence Data, Peptide Fragments, Peptide Mapping, Reference Standards, Cellular Senescence, Proteome, Proteomics, Cell Line, Tumor, Tandem Mass Spectrometry, Topoisomerase Inhibitors, Cell Cycle Checkpoints
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