This study makes me so happy!
I've been digging through the NCI-60 proteomes from Gholami et al., since they came out 5 years ago. I use this study as my favorite example of how valuable a proteomics dataset can be when done right -- you can mine them for new stuff for years and despite the fact many people have been through this one -- there is still new stuff to find.
In this new JPR study, this team does an amazing job of driving home this point. Yo -- most of these files are from an Orbi XL (select samples are also repeated with Orbitrap Elite OT/OT). They pull out all the data, intelligently combine the results of search engines search engines, incorporate RNA-Seq, and by being really smart with the data analysis find evidence of almost 200 "missing proteins".
5 of these proteins meet the guidelines the Chromosome Centric Human Proteome Project (C-HPP) has for proving presence. This is a big deal. These are proteins that genetics suggests should be present -- but you can't find mass spec data of so it's thought the genetics expression model is wrong. But -- here they are-- hiding in Orbitrap XL data that y'all can download here and look at anytime you want.
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