Sunday, December 26, 2021

Mapping the Melanoma Plasma Proteome with MS1 Transfer!


How far can we push MS1 transfer (more commonly Match Between Runs)? When we want to dig deep into the plasma proteome? These authors decided to find out with the plasma from patients with Melanoma. (I really like the plot above that shows what each plasma depletion technique starts to let you see!)

The base strategy is pretty straight-forward. They used something very similar to match between runs (using Proteome Discoverer 2.4) for multiple plasma depletion strategies as well as some work with a cancer cell line digest to get a bunch of IDs and then they transferred the MS1 peptides to the undepleted plasma using 2 hour gradients on an HF-X. FDR appears to be applied to the MS1 matches, but I'm a little fuzzy on that and the role DIA played in the study. 

Regardless, they come up with a whole pile of previously established markers for melanoma, as well digging brings up several more that look extremely promising. 

The files haven't been unlocked as of the time I'm writing this, but I'm sure they will be soon and they're at ProteomeXchange here

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