Comparing the personal proteomics project to the ‘Snyderome’
March 21, 2012
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Last week was coming out time for personal proteomics: not only have my combined and partial saliva proteome and microbioproteome results been released and the data made available but also an interesting paper including individual proteomics data from Michael Snyder has been published and announced as part of the much bigger Molecular Omics Profiling Project ( iPOP approach).
I thought it does make sense to briefly compare our methods/data/context with that of the Snyder study partially focusing on its proteomics component.
The basic similarity is that in both projects longitudinal proteomics dynamics measurements have been conducted over different time points with shotgun mass spectrometry proteomics.
The basic difference between the 2 projects concerning proteomics is that while in our case the central question is what kind of biological understanding can we gain from analysing protein data acquired via mass spec in the case of the iPOP approach proteomics was just one of the omics assayed and the results were marginal compared to the main results gained from genomic and transcriptomic data.
While we will talk about using our proteomics data in context of other data types (for instance I have already used my detected peptides and amino acids to cross validate non-synonymous SNPs coming from 23andMe genotyping data) by now we would really like to introduce and analyse mass spec proteomics data on its own so to highlight its peculiarities, strength and weakness and not mix and mask this with other type of biological data.
Another difference might be the budget used: in Snyder’s case I assume the bill was quite high, I personally don’t know the sources for sure. It seems to me like a big budget Hollywood A-list movie, say Saving Private Ryan.
In our case I personally paid ~150 GBP for the FEDEX shipment 3 times out of my pocket and Bioproximity, a small company covered all other expenses. It’s like Reservoir Dogs.
Here is an overview table comparing the 2 approaches focusing on the proteomics part.
One last important thing is data availability: while we released our data 2 different ways and made it easily available in many forms (search engine output results containing identifications, spectra files, complex pride xml files containing identifications + spectra, search database, search parameters used) so as to make it repeatable and reusable, the Snyder proteomics data was uploaded to Tranche and to this day the data seems to be encrypted and passphrase is required so it cannot be said what is there really. (Let me know if this is other way and I update the post, am just talking about my experience here with the Tranche Data, see screenshot)