Monday, December 11, 2017

The Synaptosome Proteome!

At the very top of my "favorite new (to me) field to say 3 times fast list" -- I present this awesome new study on the synaptosome proteome!

A little looking around and I had to add the "to me" part. There are dozens of studies on the proteomes of synaptic junctions going back to before I ever learned how to use a mass spec, but having not read any of the others -- this is, by far, my favorite one!


1) Real human brains were employed.
2) Even more impressive? This is tissue from a bunch of human brains with really interesting phenotypes.
3) Multi-plex iTRAQ was performed (2 4-plexes) -- and performed expertly. 8 "normal" brain controls were combined in equal ratios and these were used as channel 117 in both 4-plex groups. That's really smart, right? They could look at 6 patients from their disease state (the other 3 channels times 2) and compare it to 8 of their control groups. The control mixture in 117 can be used to normalize between the two 4-plex sets AND all interesting observations in the patient samples can be obtained by just using the 117 channel as the denominator. Simple -- and I'm totally using this later.
4) Other sample are also studied using label free quan. I have the RAW data files on my desktop, but I'm not 100% sure how the data was processed. The findings from the LFQ and the iTRAQ analysis were compared and combined.
6) PD 2.1 was used for the data analysis, and InfernoRDN (which I'd forgotten about somehow!) was uses for statistical analysis. If you don't know about this -- I highly recommend you check it out!
6) PRM was used to validate the interesting findings!
6) This data is also integrated into the C-HPP's search for missing proteins!

I can't gauge the value of their biological findings, but the samples are really cool, and the proteomics is some top-notch stuff. They point out some pathways that seem to make sense with the theme of the paper and that's good enough for me!

All the RAW data is up on ProteomeXchange (where I actually found out about this study) here. 

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