Many in the mass spectrometry community agree that MS data should be made publicly available for everybody’s benefit. All data, including the raw files generated by the mass spectrometers.
In the May editorial we support this request and introduce a new raw data repository run by the EBI that offers to replace the declining TRANCHE, up to very recently the only repository for such data.
Several good reasons can be made for making raw data available – one of them is the re-analysis of published data to validate claims. For example, the controversy arising in the wake of the analysis of fossilized Tyrannosaurus rex bones by Asara and colleagues which led them to suggest that T. rex is more closely related to birds than to reptiles (Asara et al., Science 2007). Their findings were finally corroborated in 2009 (Bern et al.; J. Proteome Res.) but could have been examined much quicker, if access to raw data had been given at the time of publication.
Re-analysis aside, raw data present a treasure trove of information that can be examined from different angles and, over time, with new tools that bring aspects to light that the original experimenters did not think of. To create such new analysis tools, software developers rely on raw data to benchmark against established techniques.
Having access to raw files does not mean that they are easy to use – we realize that the diversity in file formats and the difficulty in converting one file type to another makes their analysis not as straight forward as it could be with a single community supported format. And we also realize that these files are large and uploading them to the new EBI, or any other repository, will take time and some effort, particularly if important meta data about the experiment are included.
Still, we think the effort is worth it to ensure the field can move forward. We’d love to hear your views, particularly if you disagree.