The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Proteomic Parsimony through Bipartite Graph Analysis Improves Accuracy and Transparency
Open accessAbstract
Assembling peptides identified from LC-MS/MS spectra into a list of proteins is a critical step in analyzing shotgun proteomics data. As one peptide sequence can be mapped to multiple proteins in a database, naïve protein assembly can substantially overstate the number of proteins found in samples. We model the peptide-protein relationships in a bipartite graph and use efficient graph algorithms to identify protein clusters with shared peptides and to derive the minimal list of proteins. We test the effects of this parsimony analysis approach using MS/MS data sets generated from a defined human protein mixture, a yeast whole cell extract, and a human serum proteome after MARS column depletion. The results demonstrate that the bipartite parsimony technique not only simplifies protein lists but also improves the accuracy of protein identification. We use bipartite graphs for the visualization of the protein assembly results to render the parsimony analysis process transparent to users. Our approach also groups functionally related proteins together and improves the comprehensibility of the results. We have implemented the tool in the IDPicker package. The source code and binaries for this protein assembly pipeline are available under Mozilla Public License at the following URL: http://www.mc.vanderbilt.edu/msrc/bioinformatics/.
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Cites
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Interpretation of Shotgun Proteomic Data
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Cited by
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Tabb, D. L., Vega-Montoto, L., Rudnick, P. A., Variyath, A. M., Ham, A.-J. L., Bunk, D. M., Kilpatrick, L. E., Billheimer, D. D., Blackman, R. K., Cardasis, H. L., et al. (2010) · Journal of Proteome Research · doi:10.1021/pr9006365 · Cited by 551
Self-citationDepletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics
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Proteogenomic Characterization of Human Early-Onset Gastric Cancer
Mun, D.-G., Bhin, J., Kim, S., Kim, H., Jung, J. H., Jung, Y., Jang, Y. E., Park, J. M., Kim, H., Jung, Y., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2018.12.003 · Cited by 294
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
Boyken, S. E., Chen, Z., Groves, B., Langan, R. A., Oberdorfer, G., Ford, A., Gilmore, J. M., Xu, C., DiMaio, F., Pereira, J. H., et al. (2016) · Science · doi:10.1126/science.aad8865 · Cited by 304
Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0
Carvalho, P. C., Lima, D. B., Leprevost, F. V., Santos, M. D. M., Fischer, J. S. G., Aquino, P. F., Moresco, J. J., Yates, J. R., & Barbosa, V. C. (2016) · Nature Protocols · doi:10.1038/nprot.2015.133 · Cited by 283
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Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data
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Differential localization and dynamics of class I myosins in the enterocyte microvillus
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Self-citationVincow, E. S., Thomas, R. E., Merrihew, G. E., Shulman, N. J., Bammler, T. K., MacDonald, J. W., MacCoss, M. J., & Pallanck, L. J. (2019) · Autophagy · doi:10.1080/15548627.2019.1586258 · Cited by 54
Yugandhar, K., Gupta, S., & Yu, H. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.05.007 · Cited by 51
“…from remaining spectra Scaffold [107] “ Greedy ” approach “ One-hit ” wonders ProteinProphet [105] Employs a probability-based model IDPicker [109] Performs better than both “ two-peptide ” and “ one peptide ” rule HIquant [111] Bottom-up approach; requires corresponding ion ratios MRM [115]…”
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Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection
Wojcik, R., Li, Y., MacCoss, M. J., & Dovichi, N. J. (2012) · Talanta · doi:10.1016/j.talanta.2011.10.048 · Cited by 43
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Metadata
- Authors
- Zhang, B., Chambers, M. C., & Tabb, D. L.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-08-04
- Volume
- 6
- Issue
- 9
- Pages
- 3549-3557
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W1990273811
- Cited by
- 373
- References
- 2
- FWCI
- 9.00
- Type
- journal article
- Language
- en
- Open access
- green
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