The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
Open accessAbstract
Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ± 500 Da. In a proteome-wide data set on HEK293 cells (9,513 proteins and 396,736 peptides), this approach matched an additional 184,000 modified peptides, which were linked to biological and chemical modifications representing 523 distinct mass bins, including phosphorylation, glycosylation and methylation. We localized all unknown modification masses to specific regions within a peptide. Known modifications were assigned to the correct amino acids with frequencies >90%. We conclude that at least one-third of unassigned spectra arise from peptides with substoichiometric modifications.
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Self-citationBeausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577
Self-citationDeep proteome and transcriptome mapping of a human cancer cell line
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The quantitative proteome of a human cell line
Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., & Aebersold, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.82 · Cited by 816
Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014050 · Cited by 797
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Rebak, A. S., Hendriks, I. A., Elsborg, J. D., Buch-Larsen, S. C., Nielsen, C. H., Terslev, L., Kirsch, R., Damgaard, D., Doncheva, N. T., Lennartsson, C., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01214-9 · Cited by 45
Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics
Cifani, P., Li, Z., Luo, D., Grivainis, M., Intlekofer, A. M., Fenyö, D., & Kentsis, A. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00638 · Cited by 24
C-terminal amides mark proteins for degradation via SCF/FBXO31
Muhar, M., Farnung, J., Hofmann, R., Cernakova, M., Sidiropoulos, N. D., Bode, J. W., & Corn, J. E. (2023) · doi:10.1101/2023.06.29.547030 · Cited by 5
Metadata
- Authors
- Chick, J. M., Kolippakkam, D., Nusinow, D. P., Zhai, B., Rad, R., Huttlin, E. L., & Gygi, S. P.
- Venue
- Nature Biotechnology
- Published
- 2015-06-15
- Volume
- 33
- Issue
- 7
- Pages
- 743-749
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1480858518
- Cited by
- 425
- References
- 5
- FWCI
- 18.54
- Type
- journal article
- Language
- en
- Open access
- green
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