Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
- Author
- Ralf Gabriels (UGent) , Lennart Martens (UGent) and Sven Degroeve (UGent)
- Organization
- Abstract
- (MSPIP)-P-2 is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the (MSPIP)-P-2 web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we have added specialized models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides, and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run (MSPIP)-P-2, and have completely rebuilt the web server, which now allows predictions of up to 100 000 peptide sequences in a single request. The MS(2)PIPweb server is freely available at https://iomics.ugent.be/ms2pip/.
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MS2PIP 2019 NAR Published version.pdf
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MS2PIP 2019 Supplementary figures Revision 2.pdf
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8616058
- MLA
- Gabriels, Ralf, et al. “Updated MS2PIP Web Server Delivers Fast and Accurate MS2 Peak Intensity Prediction for Multiple Fragmentation Methods, Instruments and Labeling Techniques.” NUCLEIC ACIDS RESEARCH, vol. 47, no. W1, 2019, pp. W295–99, doi:10.1093/nar/gkz299.
- APA
- Gabriels, R., Martens, L., & Degroeve, S. (2019). Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. NUCLEIC ACIDS RESEARCH, 47(W1), W295–W299. https://doi.org/10.1093/nar/gkz299
- Chicago author-date
- Gabriels, Ralf, Lennart Martens, and Sven Degroeve. 2019. “Updated MS2PIP Web Server Delivers Fast and Accurate MS2 Peak Intensity Prediction for Multiple Fragmentation Methods, Instruments and Labeling Techniques.” NUCLEIC ACIDS RESEARCH 47 (W1): W295–99. https://doi.org/10.1093/nar/gkz299.
- Chicago author-date (all authors)
- Gabriels, Ralf, Lennart Martens, and Sven Degroeve. 2019. “Updated MS2PIP Web Server Delivers Fast and Accurate MS2 Peak Intensity Prediction for Multiple Fragmentation Methods, Instruments and Labeling Techniques.” NUCLEIC ACIDS RESEARCH 47 (W1): W295–W299. doi:10.1093/nar/gkz299.
- Vancouver
- 1.Gabriels R, Martens L, Degroeve S. Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. NUCLEIC ACIDS RESEARCH. 2019;47(W1):W295–9.
- IEEE
- [1]R. Gabriels, L. Martens, and S. Degroeve, “Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques,” NUCLEIC ACIDS RESEARCH, vol. 47, no. W1, pp. W295–W299, 2019.
@article{8616058,
abstract = {{(MSPIP)-P-2 is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the (MSPIP)-P-2 web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we have added specialized models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides, and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run (MSPIP)-P-2, and have completely rebuilt the web server, which now allows predictions of up to 100 000 peptide sequences in a single request. The MS(2)PIPweb server is freely available at https://iomics.ugent.be/ms2pip/.}},
author = {{Gabriels, Ralf and Martens, Lennart and Degroeve, Sven}},
issn = {{0305-1048}},
journal = {{NUCLEIC ACIDS RESEARCH}},
language = {{eng}},
number = {{W1}},
pages = {{W295--W299}},
title = {{Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques}},
url = {{http://doi.org/10.1093/nar/gkz299}},
volume = {{47}},
year = {{2019}},
}
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