The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens
- Author
- Panayotis Vlastaridis, Stephen G Oliver, Yves Van de Peer (UGent) and Grigoris D Amoutzias
- Organization
- Project
- Abstract
- During the last decade, there has been great progress in high-throughput (HTP) phosphoproteomics and hundreds or even thousands of phosphorylation sites (p-sites) can now be detected in a single experiment. This success is attributable to a combination of very sensitive Mass Spectrometry instruments, better phosphopeptide enrichment techniques and bioinformatics software that are capable of detecting peptides and localizing p-sites. These new technologies have opened up a whole new level of gene regulation to be studied, with great potential for therapeutics and synthetic biology. Nevertheless, many challenges remain to be resolved; these concern the biases and noise of these proteomic technologies, the biological noise that is present, as well as the incompleteness of the current datasets. Despite these problems, the datasets published so far appear to represent a good sample of a complete phosphoproteome of some organisms and are capable of revealing their major properties.
- Keywords
- Phosphoproteomics, Phosphorylation, Bioinformatics, Data integration
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8500088
- MLA
- Vlastaridis, Panayotis, et al. “The Challenges of Interpreting Phosphoproteomics Data : A Critical View through the Bioinformatics Lens.” Lecture Notes in Computer Science, edited by Claudia Angelini et al., vol. 9874, Springer, 2016, pp. 196–204, doi:10.1007/978-3-319-44332-4_15.
- APA
- Vlastaridis, P., Oliver, S. G., Van de Peer, Y., & Amoutzias, G. D. (2016). The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens. In C. Angelini, P. M. Rancoita, & S. Rovetta (Eds.), Lecture Notes in Computer Science (Vol. 9874, pp. 196–204). https://doi.org/10.1007/978-3-319-44332-4_15
- Chicago author-date
- Vlastaridis, Panayotis, Stephen G Oliver, Yves Van de Peer, and Grigoris D Amoutzias. 2016. “The Challenges of Interpreting Phosphoproteomics Data : A Critical View through the Bioinformatics Lens.” In Lecture Notes in Computer Science, edited by Claudia Angelini, Paola MV Rancoita, and Stefano Rovetta, 9874:196–204. Cham, Switzerland: Springer. https://doi.org/10.1007/978-3-319-44332-4_15.
- Chicago author-date (all authors)
- Vlastaridis, Panayotis, Stephen G Oliver, Yves Van de Peer, and Grigoris D Amoutzias. 2016. “The Challenges of Interpreting Phosphoproteomics Data : A Critical View through the Bioinformatics Lens.” In Lecture Notes in Computer Science, ed by. Claudia Angelini, Paola MV Rancoita, and Stefano Rovetta, 9874:196–204. Cham, Switzerland: Springer. doi:10.1007/978-3-319-44332-4_15.
- Vancouver
- 1.Vlastaridis P, Oliver SG, Van de Peer Y, Amoutzias GD. The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens. In: Angelini C, Rancoita PM, Rovetta S, editors. Lecture Notes in Computer Science. Cham, Switzerland: Springer; 2016. p. 196–204.
- IEEE
- [1]P. Vlastaridis, S. G. Oliver, Y. Van de Peer, and G. D. Amoutzias, “The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens,” in Lecture Notes in Computer Science, Naples, Italy, 2016, vol. 9874, pp. 196–204.
@inproceedings{8500088,
abstract = {{During the last decade, there has been great progress in high-throughput (HTP) phosphoproteomics and hundreds or even thousands of phosphorylation sites (p-sites) can now be detected in a single experiment. This success is attributable to a combination of very sensitive Mass Spectrometry instruments, better phosphopeptide enrichment techniques and bioinformatics software that are capable of detecting peptides and localizing p-sites. These new technologies have opened up a whole new level of gene regulation to be studied, with great potential for therapeutics and synthetic biology. Nevertheless, many challenges remain to be resolved; these concern the biases and noise of these proteomic technologies, the biological noise that is present, as well as the incompleteness of the current datasets. Despite these problems, the datasets published so far appear to represent a good sample of a complete phosphoproteome of some organisms and are capable of revealing their major properties.}},
author = {{Vlastaridis, Panayotis and Oliver, Stephen G and Van de Peer, Yves and Amoutzias, Grigoris D}},
booktitle = {{Lecture Notes in Computer Science}},
editor = {{Angelini, Claudia and Rancoita, Paola MV and Rovetta, Stefano}},
isbn = {{9783319443317}},
issn = {{0302-9743}},
keywords = {{Phosphoproteomics,Phosphorylation,Bioinformatics,Data integration}},
language = {{eng}},
location = {{Naples, Italy}},
pages = {{196--204}},
publisher = {{Springer}},
title = {{The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens}},
url = {{http://doi.org/10.1007/978-3-319-44332-4_15}},
volume = {{9874}},
year = {{2016}},
}
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