The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Enhanced Global Post-translational Modification Discovery with MetaMorpheus
Abstract
Correct identification of protein post-translational modifications (PTMs) is crucial to understanding many aspects of protein function in biological processes. G-PTM-D is a recently developed technique for global identification and localization of PTMs. Spectral file calibration prior to applying G-PTM-D, and algorithmic enhancements in the peptide database search significantly increase the accuracy, speed, and scope of PTM identification. We enhance G-PTM-D by using multinotch searches and demonstrate its effectiveness in identification of numerous types of PTMs including high-mass modifications such as glycosylations. The changes described in this work lead to a 20% increase in the number of identified modifications and an order of magnitude decrease in search time. The complete workflow is implemented in MetaMorpheus, a software tool that integrates the database search procedure, identification of coisolated peptides, spectral calibration, and the enhanced G-PTM-D workflow. Multinotch searches are also shown to be useful in contexts other than G-PTM-D by producing superior results when used instead of standard narrow-window and open database searches.
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Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Senko, M. W., Beu, S. C., & McLaffertycor, F. W. (1995) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(95)00017-8 · Cited by 451
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq
Sheynkman, G. M., Shortreed, M. R., Frey, B. L., & Smith, L. M. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.028142 · Cited by 128
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Frankenfield, A. M., Ni, J., Ahmed, M., & Hao, L. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00145 · Cited by 321
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Chen, C., Hou, J., Tanner, J. J., & Cheng, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082873 · Cited by 280
Identification and Quantification of Proteoforms by Mass Spectrometry
Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., et al. (2019) · PROTEOMICS · doi:10.1002/pmic.201800361 · Cited by 209
Self-citationRoberts, D. S., Loo, J. A., Tsybin, Y. O., Liu, X., Wu, S., Chamot-Rooke, J., Agar, J. N., Paša-Tolić, L., Smith, L. M., & Ge, Y. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00318-2 · Cited by 161
Self-citationValdés-Mas, R., Leshem, A., Zheng, D., Cohen, Y., Kern, L., Zmora, N., He, Y., Katina, C., Eliyahu-Miller, S., Yosef-Hevroni, T., et al. (2025) · Cell · doi:10.1016/j.cell.2024.12.016 · Cited by 89
Metadata
- Authors
- Solntsev, S. K., Shortreed, M. R., Frey, B. L., & Smith, L. M.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-03-26
- Volume
- 17
- Issue
- 5
- Pages
- 1844-1851
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2789457189
- Cited by
- 262
- References
- 3
- FWCI
- 9.77
- Type
- journal article
- Language
- en
- Open access
- closed
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