Mango proteomics/glycoproteomics study shows we don't need genomics people anymore!

I liked this study so much that I wrote a commentary for this weird Proteomics journal, but I think they must have hated it because it's been sitting as "Accepted" for like 2 months. I might have been super jetlagged in Europe and forcing myself to stay up all day and mildly hallucinating while reading Tolkien and it might show in the commentary. 

So maybe what I'll type here about this great study will be more coherent. 

We've been looking at some less well annotated organisms recently and I feel like the genomics people are really sort of mailing it in right now. They're sequencing all the things, and as long as they deposit their half aligned crap on GigaDB and they get a BUSCO score of greater than 80% (this means they are able to find the majority of genes that we know need to be there for something to be alive, you know like the ribosomes and TCA cycle enzymes, that stuff) they can deposit crap.

Why would I think it's crap? Well...if you predict open reading frames and more than half of them for a eukaryote don't start with a methionine, chances are you found the wrong calling in your career. 

The reason I really liked this new study is that the mango genome is crap. And this team was like - we don't even care. Our proteomics is so good that we're not only going to identify proteins that change as mangos ripen, we're also going to do the glycoproteomics -- ON A CRAPPY FASTA? 

And it works. And it's really good. For mass spec nerds you might be more interested in the comparison of TMT-SPS-MS3 and LFQ based quan for underannotated organisms. Both datasets are really good and overlap well. The glyco is awesome, though. And they really tweak things to dig deep into the N-glycans.