This document provides comprehensive citations for all algorithms implemented in the onsite package, including original manuscripts, related work, and implementation references.
Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006). A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature Biotechnology, 24(10), 1285-1292.
DOI: 10.1038/nbt1240
BibTeX:
@article{beausoleil2006probability,
title={A probability-based approach for high-throughput protein phosphorylation analysis and site localization},
author={Beausoleil, Sean A and Vill{\'e}n, Judit and Gerber, Scott A and Rush, John and Gygi, Steven P},
journal={Nature Biotechnology},
volume={24},
number={10},
pages={1285--1292},
year={2006},
publisher={Nature Publishing Group}
}
Taus, T., Köcher, T., Pichler, P., Paschke, C., Schmidt, A., Henrich, C., & Mechtler, K. (2011). Universal and confident phosphorylation site localization using phosphoRS. Journal of Proteome Research, 10(12), 5354-5362.
DOI: 10.1021/pr200611n
BibTeX:
@article{taus2011universal,
title={Universal and confident phosphorylation site localization using phosphoRS},
author={Taus, Thomas and K{\"o}cher, Thomas and Pichler, Peter and Paschke, Christian and Schmidt, Andreas and Henrich, Christian and Mechtler, Karl},
journal={Journal of Proteome Research},
volume={10},
number={12},
pages={5354--5362},
year={2011},
publisher={ACS Publications}
}
LuciPHOr (2013): Fermin, D., Walmsley, S. J., Gingras, A. C., Choi, H., & Nesvizhskii, A. I. (2013). LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Molecular & Cellular Proteomics, 12(11), 3409-3419.
DOI: 10.1074/mcp.M113.028928
BibTeX:
@article{fermin2013luciphor,
title={LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach},
author={Fermin, Damian and Walmsley, Scott J and Gingras, Anne-Claude and Choi, Hyungwon and Nesvizhskii, Alexey I},
journal={Molecular \& Cellular Proteomics},
volume={12},
number={11},
pages={3409--3419},
year={2013},
doi={10.1074/mcp.M113.028928}
}
LuciPHOr2 (2015): Fermin, D., Avtonomov, D., Choi, H., & Nesvizhskii, A. I. (2015). LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data. Bioinformatics, 31(7), 1141-1143.
DOI: 10.1093/bioinformatics/btu788
BibTeX:
@article{fermin2015luciphor2,
title={LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data},
author={Fermin, Damian and Avtonomov, Dmitry and Choi, Hyungwon and Nesvizhskii, Alexey I},
journal={Bioinformatics},
volume={31},
number={7},
pages={1141--1143},
year={2015},
doi={10.1093/bioinformatics/btu788}
}
Röst, H. L., Sachsenberg, T., Aiche, S., Bielow, C., Weisser, H., Aicheler, F., Andreotti, S., Ehrlich, H. C., Gutenbrunner, P., Kenar, E., Liang, X., Nahnsen, S., Nilse, L., Pfeuffer, J., Rosenberger, G., Rurik, M., Schmitt, U., Veit, J., Walzer, M., Wojnar, D., Wolski, W. E., Schilling, O., Choudhary, J. S., Malmström, L., Aebersold, R., Reinert, K., & Kohlbacher, O. (2016). OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods, 13(9), 741-748.
DOI: 10.1038/nmeth.3959
Kohlbacher, O., Reinert, K., Gröpl, C., Lange, E., Pfeifer, N., Schulz-Trieglaff, O., & Sturm, M. (2007). TOPP–the OpenMS proteomics pipeline. Bioinformatics, 23(2), e191-e197.
DOI: 10.1093/bioinformatics/btl299
Barsnes, H., Vaudel, M., Colaert, N., Helsens, K., Sickmann, A., Berven, F. S., & Martens, L. (2011). compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics, 12, 70.
DOI: 10.1186/1471-2105-12-70
Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., Kern, R., Picus, M., Hoyer, S., van Kerkwijk, M. H., Brett, M., Haldane, A., Del Río, J. F., Wiebe, M., Peterson, P., Gérard-Marchant, P., Sheppard, K., Reddy, T., Weckesser, W., Abbasi, H., Gohlke, C., & Oliphant, T. E. (2020). Array programming with NumPy. Nature, 585(7825), 357-362.
DOI: 10.1038/s41586-020-2649-2
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., van der Walt, S. J., Brett, M., Wilson, J., Millman, K. J., Mayorov, N., Nelson, A. R. J., Jones, E., Kern, R., Larson, E., Carey, C. J., Polat, İ., Feng, Y., Moore, E. W., VanderPlas, J., Laxalde, D., Perktold, J., Cimrman, R., Henriksen, I., Quintero, E. A., Harris, C. R., Archibald, A. M., Ribeiro, A. H., Pedregosa, F., van Mulbregt, P., & SciPy 1.0 Contributors. (2020). SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17(3), 261-272.
DOI: 10.1038/s41592-019-0686-2
If you use onsite in your research, please cite:
onsite: Mass spectrometry post-translational
modification localization tool. https://github.com/bigbio/onsite
Beausoleil, S. A., et al. (2006). A probability-based approach for high-throughput
protein phosphorylation analysis and site localization. Nature Biotechnology,
24(10), 1285-1292.
Taus, T., et al. (2011). Universal and confident phosphorylation site
localization using phosphoRS. Journal of Proteome Research, 10(12), 5354-5362.
Fermin, D., Walmsley, S. J., Gingras, A. C., Choi, H., & Nesvizhskii, A. I. (2013).
LuciPHOr: algorithm for phosphorylation site localization with false localization rate
estimation using modified target-decoy approach. Molecular & Cellular Proteomics,
12(11), 3409-3419.
Fermin, D., Avtonomov, D., Choi, H., & Nesvizhskii, A. I. (2015). LuciPHOr2: site
localization of generic post-translational modifications from tandem mass spectrometry
data. Bioinformatics, 31(7), 1141-1143.
This software is licensed under the MIT License. See the LICENSE file for details.
onsite builds upon the excellent work of the original algorithm developers and the OpenMS community. We thank all contributors and users for their feedback and support.
We welcome contributions to onsite. Please see our Contributing Guidelines for more information.