The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
Accurate and Sensitive Peptide Identification with Mascot Percolator
Open accessAbstract
Sound scoring methods for sequence database search algorithms such as Mascot and Sequest are essential for sensitive and accurate peptide and protein identifications from proteomic tandem mass spectrometry data. In this paper, we present a software package that interfaces Mascot with Percolator, a well performing machine learning method for rescoring database search results, and demonstrate it to be amenable for both low and high accuracy mass spectrometry data, outperforming all available Mascot scoring schemes as well as providing reliable significance measures. Mascot Percolator can be readily used as a stand alone tool or integrated into existing data analysis pipelines.
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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TANDEM: matching proteins with tandem mass spectra
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Semi-supervised learning for peptide identification from shotgun proteomics datasets
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Cited by
Zhang, J., Xin, L., Shan, B., Chen, W., Xie, M., Yuen, D., Zhang, W., Zhang, Z., Lajoie, G. A., & Ma, B. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.010587 · Cited by 1,081
Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034769 · Cited by 528
“For the one hour experiments, between three and eight dubious ORFs were identified per dataset (Table I), confirming these data are indeed well below the 1% FDR threshold.”
MethodInfluentialKelmer Sacramento, E., Kirkpatrick, J. M., Mazzetto, M., Baumgart, M., Bartolome, A., Di Sanzo, S., Caterino, C., Sanguanini, M., Papaevgeniou, N., Lefaki, M., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209596 · Cited by 236
Brosch, M., Saunders, G. I., Frankish, A., Collins, M. O., Yu, L., Wright, J., Verstraten, R., Adams, D. J., Harrow, J., Choudhary, J. S., et al. (2011) · Genome Research · doi:10.1101/gr.114272.110 · Cited by 130
Self-citationSchüler, S. C., Kirkpatrick, J. M., Schmidt, M., Santinha, D., Koch, P., Di Sanzo, S., Cirri, E., Hemberg, M., Ori, A., & von Maltzahn, J. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109223 · Cited by 106
Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging
Heinze, I., Bens, M., Calzia, E., Holtze, S., Dakhovnik, O., Sahm, A., Kirkpatrick, J. M., Szafranski, K., Romanov, N., Sama, S. N., et al. (2018) · BMC Biology · doi:10.1186/s12915-018-0547-y · Cited by 65
Niere, F., Namjoshi, S., Song, E., Dilly, G. A., Schoenhard, G., Zemelman, B. V., Mechref, Y., & Raab-Graham, K. F. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.055079 · Cited by 38
“The identification of proteins/peptides was achieved using MASCOT database (40).”
MethodConserved exchange of paralog proteins during neuronal differentiation
Di Fraia, D., Anitei, M., Mackmull, M.-T., Parca, L., Behrendt, L., Andres-Pons, A., Gilmour, D., Helmer Citterich, M., Kaether, C., Beck, M., et al. (2022) · Life Science Alliance · doi:10.26508/lsa.202201397 · Cited by 2
Metadata
- Authors
- Brosch, M., Yu, L., Hubbard, T., & Choudhary, J.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-05-08
- Volume
- 8
- Issue
- 6
- Pages
- 3176-3181
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W1996701734
- Cited by
- 428
- References
- 27
- FWCI
- 4.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
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