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Exploring the potential of public proteomics data

(2016) PROTEOMICS. 16(2). p.214-225
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Abstract
In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.
Keywords
Bioinformatics, Computational proteomics, Data analysis, Databases, Data standards, MASS-SPECTROMETRY DATA, PHOSPHORYLATION SITE LOCALIZATION, PROTEIN-CODING GENES, SHOTGUN PROTEOMICS, POSTTRANSLATIONAL MODIFICATIONS, TYRANNOSAURUS-REX, PHOSPHOPROTEOMICS DATA, SPECTRAL ARCHIVES, DATA REPOSITORIES, PRIDE CONVERTER

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Citation

Please use this url to cite or link to this publication:

MLA
Vaudel, Marc, Kenneth Verheggen, Attila Csordas, et al. “Exploring the Potential of Public Proteomics Data.” PROTEOMICS 16.2 (2016): 214–225. Print.
APA
Vaudel, M., Verheggen, K., Csordas, A., Raeder, H., Berven, F. S., Martens, L., Vizcaíno, J. A., et al. (2016). Exploring the potential of public proteomics data. PROTEOMICS, 16(2), 214–225.
Chicago author-date
Vaudel, Marc, Kenneth Verheggen, Attila Csordas, Helge Raeder, Frode S Berven, Lennart Martens, Juan A Vizcaíno, and Harald Barsnes. 2016. “Exploring the Potential of Public Proteomics Data.” Proteomics 16 (2): 214–225.
Chicago author-date (all authors)
Vaudel, Marc, Kenneth Verheggen, Attila Csordas, Helge Raeder, Frode S Berven, Lennart Martens, Juan A Vizcaíno, and Harald Barsnes. 2016. “Exploring the Potential of Public Proteomics Data.” Proteomics 16 (2): 214–225.
Vancouver
1.
Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, et al. Exploring the potential of public proteomics data. PROTEOMICS. 2016;16(2):214–25.
IEEE
[1]
M. Vaudel et al., “Exploring the potential of public proteomics data,” PROTEOMICS, vol. 16, no. 2, pp. 214–225, 2016.
@article{8572825,
  abstract     = {{In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.}},
  author       = {{Vaudel, Marc and Verheggen, Kenneth and Csordas, Attila and Raeder, Helge and Berven, Frode S and Martens, Lennart and Vizcaíno, Juan A and Barsnes, Harald}},
  issn         = {{1615-9853}},
  journal      = {{PROTEOMICS}},
  keywords     = {{Bioinformatics,Computational proteomics,Data analysis,Databases,Data standards,MASS-SPECTROMETRY DATA,PHOSPHORYLATION SITE LOCALIZATION,PROTEIN-CODING GENES,SHOTGUN PROTEOMICS,POSTTRANSLATIONAL MODIFICATIONS,TYRANNOSAURUS-REX,PHOSPHOPROTEOMICS DATA,SPECTRAL ARCHIVES,DATA REPOSITORIES,PRIDE CONVERTER}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{214--225}},
  title        = {{Exploring the potential of public proteomics data}},
  url          = {{http://dx.doi.org/10.1002/pmic.201500295}},
  volume       = {{16}},
  year         = {{2016}},
}

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