The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry
Open accessPreprint — published as 10.1021/acs.jproteome.0c00952
Abstract
Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complimentary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum.
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Cites
How many human proteoforms are there?
Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2576 · Cited by 907
Self-citationTop Down proteomics: Facts and perspectives
Catherman, A. D., Skinner, O. S., & Kelleher, N. L. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.02.041 · Cited by 507
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Metadata
- Authors
- Lantz, C., Zenaidee, M. A., Wei, B., Hemminger, Z., R. Ogorzalek Loo, R., & Loo, J.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Loo, Joseph
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2021-01-05
- Volume
- 20
- Issue
- 4
- Pages
- 1928-1935
- ISSN
- 1535-3893 (ISSN-L)
- PMC
- PMC8174100
- OpenAlex
- W3134982166
- Cited by
- 72
- References
- 2
- Citations by year
- 2026: 9 · 2025: 17 · 2024: 16 · 2023: 13 · 2022: 12 · 2021: 5
- FWCI
- 4.19
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Proteome Research (publishedVersion)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Royal College of Surgeons in Ireland (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation (GM007185, DE-FC02-02ER63421, 1808492, R01GM103479)
- U.S. Department of Energy (DEFC0202ER63421, FC02-02ER63421)
- National Institutes of Health (DE-FC02-02ER63421)
- National Institute of General Medical Sciences (GM 007185, R01GM103479, T32GM007185)
- National Center for Research Resources (S10RR028893)
- Division of Chemistry (CHE-1808492)
- 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 mass spectrometry, peptide identification, methionine oxidation, sequencing depth
- MeSH terms
- Algorithms, Amino Acid Sequence, Myoglobin, Peptides, Mass Spectrometry
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