Top‐down protein identification of proteasome proteins with nanoLC‐FT‐ICR‐MS employing data‐independent fragmentation methods
Open accessAbstract
A comparison of different data‐independent fragmentation methods combined with LC coupled to high‐resolution FT‐ICR‐MS/MS is presented for top‐down MS of protein mixtures. Proteins composing the 20S and 19S proteasome complexes and their PTMs were identified using a 15 T FT‐ICR mass spectrometer. The data‐independent fragmentation modes with LC timescales allowed for higher duty‐cycle measurements that better suit online LC‐FT‐ICR‐MS. Protein top‐down dissociation was effected by funnel‐skimmer collisionally activated dissociation (FS‐CAD) and CASI (continuous accumulation of selected ions)‐CAD. The N‐termini for 9 of the 14 20S proteasome proteins were found to be modified, and the α3 protein was found to be phosphorylated; these results are consistent with previous reports. Mass‐measurement accuracy with the LC‐FT‐ICR system for the 20‐ to 30‐kDa 20S proteasome proteins was 1 ppm. The intact mass of the 100‐kDa Rpn1 subunit from the 19S proteasome complex regulatory particle was measured with a deviation of 17 ppm. The CASI‐CAD technique is a complementary tool for intact‐protein fragmentation and is an effective addition to the growing inventory of dissociation methods that are compatible with online protein separation coupled to FT‐ICR‐MS.
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Data-independent fragmentation in past top-down MS studies relied on in-source fragmentation of all intact proteoforms ionized simultaneously after LC elution, with no m/z filtering and limited possibility of obtaining precursor information.
“those works relied on the in-source fragmentation of all intact proteoforms ionized simultaneously after LC elution, with no m/z filtering and limited possibility of obtaining precursor information.”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [47]
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- Authors
- Lakshmanan, R., Wolff, J. J., Alvarado, R., & Loo, J. A.
- Affiliations
- University of California, Los Angeles (US)
- Bruker (United States) (US)
- Corresponding author
- Loo, Joseph A.
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2014-03-26
- Volume
- 14
- Issue
- 10
- Pages
- 1271-1282
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- PMC
- PMC4045009
- OpenAlex
- W1997240024
- Cited by
- 24
- References
- 51
- Citations by year
- 2024: 2 · 2023: 3 · 2022: 2 · 2020: 5 · 2019: 1 · 2018: 2 · 2017: 2 · 2016: 4 · 2015: 2 · 2014: 1
- FWCI
- 1.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- PROTEOMICS (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- US National Institutes of Health (R01 GM103479, S10 RR023045, S10 RR028893)
- 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, proteasome, 20S proteasome, N-terminal modification, phosphorylation, RPN1, post-translational modification
- MeSH terms
- Chromatography, Liquid, Humans, Peptide Fragments, Spectrometry, Mass, Electrospray Ionization, Proteomics, Proteasome Endopeptidase Complex, Tandem Mass Spectrometry
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