The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
A guided tour of the Trans‐Proteomic Pipeline
Open accessAbstract
The Trans‐Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein‐level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.
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Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationElias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
ProteoWizard: open source software for rapid proteomics tools development
Kessner, D., Chambers, M., Burke, R., Agus, D., & Mallick, P. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn323 · Cited by 2,024
Cited by
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He, W.-T., Wan, H., Hu, L., Chen, P., Wang, X., Huang, Z., Yang, Z.-H., Zhong, C.-Q., & Han, J. (2015) · Cell Research · doi:10.1038/cr.2015.139 · Cited by 2,517
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2557 · Cited by 1,686
Self-citationProtein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
MS-GF+ makes progress towards a universal database search tool for proteomics
Kim, S., & Pevzner, P. A. (2014) · Nature Communications · doi:10.1038/ncomms6277 · Cited by 1,098
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801
Metadata
- Authors
- Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J. K., Martin, D. B., Nesvizhskii, A. I., & Aebersold, R.
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2010-03
- Volume
- 10
- Issue
- 6
- Pages
- 1150-1159
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- OpenAlex
- W2137043026
- Cited by
- 745
- References
- 4
- FWCI
- 27.08
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J. K., Martin, D. B., Nesvizhskii, A. I., & Aebersold, R. (2010). A guided tour of the Trans‐Proteomic Pipeline. PROTEOMICS. https://doi.org/10.1002/pmic.200900375
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