Thursday, July 6, 2017

The developmental proteome of Drosophila over 15 life stages!

Drosophila melanogaster is the geneticists tool! What is someone doing stealing it and doing protein work on it?!?  Oh, you know, just finding out more about it than we ever knew!

You can check it out in this new paper in GENOME RESEARCH (yeah!) here!

They sampled fruit flies at 15 stages of their development -- including early stages that have nauseating names like "pupae". They harvested this grossness and used 2 different protein extraction techniques. I'm just a little unclear on this, but it appears that the early embryonic stage organisms need to have the proteins extracted in a different way. Dechlorination is involved. The proteins were separated in the first dimension with SDS-PAGE and peptides digested out for 280 min nanoLC runs into a quadrupole Orbitrap (plus) system running a standard Top15 method.

The resulting output? 8 MILLION high resolution MS/MS spectra. The data was all processed in MaxQuant using LFQ and all the downstream stuff was done in R.

Nearly 8,000 proteins were monitored across the life cycle. In case you're wondering, a study at MaxPlanck using GFP tagged proteins thinks that there are around 10,000 drosophila proteins. Considering that GFP tagging into the genome would put a tag separately on two proteins with 100% homology... 8,000 is probably pretty darned close to the whole thing. why is this cool? I'm sure there's some genomics/transcriptomics resource for every stage of development in fruit flies that has been around for years, right?

They track a bunch of proteoforms.
They establish the existence of some small proteins flagged as noncoding by the genetics
They find clear discrepancies between the mRNA expression levels and what is clearly the protein level expression. (Yeah!)

All the RAW data is available at ProteomeXchange PXD005691 and PXD005713

Better yet, all the expression data is easily searchable in their handy web interface that you can access here!

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