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Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites

Nature Methods volume 9, pages 771–772 (2012)Cite this article

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To the Editor:

A recent editorial in Nature Methods1 stated that proteomics raw “data can be reprocessed with new questions in mind, such as examining different post-translational modifications than the original study.” In our view, this will be the main contribution to biology arising from the reprocessing of raw data. A significant percentage of fragmentation spectra generated by shotgun proteomics remains unassigned, which leaves space for other scientists to use their creativity and knowledge to extract additional information by developing and implementing sophisticated data analysis strategies. However, the lack of a suitable repository that allows easy deposition and access to this data has discouraged many scientists from sharing and reprocessing raw data. Here we show the utility of raw data by obtaining insight into adenosine diphosphate (ADP)-ribosylation via reanalysis of a phosphoproteomics data set.

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Figure 1: Fragmentation spectra of a modified peptide derived from SERPINA3K.

References

  1. Anonymous. Nat. Methods 9, 419 (2012).

  2. Hengel, S.M. & Goodlett, D.R. Int. J. Mass Spectrom. 312, 114–121 (2012).

    Article  CAS  Google Scholar 

  3. Laing, S., Koch-Nolte, F., Haag, F. & Buck, F. J. Proteomics 75, 169–176 (2011).

    Article  CAS  Google Scholar 

  4. Huttlin, E.L. et al. Cell 143, 1174–1189 (2010).

    Article  CAS  Google Scholar 

  5. Laing, S., Unger, M., Koch-Nolte, F. & Haag, F. Amino Acids 41, 257–269 (2011).

    Article  CAS  Google Scholar 

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Acknowledgements

The authors thank M.H. Tatham and M. Trost for comments on the manuscript. This work was supported by a Sir Henry Wellcome Fellowship awarded by the Wellcome Trust (sponsor reference 088957/Z/09/Z, to I.M.)

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Authors and Affiliations

  1. Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Scotland, UK

    Ivan Matic & Ronald T Hay

  2. Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK

    Ivan Ahel

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  1. Ivan Matic
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  2. Ivan Ahel
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  3. Ronald T Hay
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Correspondence to Ivan Matic.

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Matic, I., Ahel, I. & Hay, R. Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat Methods 9, 771–772 (2012). https://doi.org/10.1038/nmeth.2106

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