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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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Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
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
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979
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
Cited by
Mass-spectrometric exploration of proteome structure and function
Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334
Frankenfield, A. M., Ni, J., Ahmed, M., & Hao, L. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00145 · Cited by 321
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling
Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265
Doellinger, J., Schneider, A., Hoeller, M., & Lasch, P. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001616 · Cited by 246
Assembling the Community-Scale Discoverable Human Proteome
Wang, M., Wang, J., Carver, J., Pullman, B. S., Cha, S. W., & Bandeira, N. (2018) · Cell Systems · doi:10.1016/j.cels.2018.08.004 · Cited by 201
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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