I legitimately thought this was going to be one of those silly mass spec things we all do where we tinker with settings and get 5% more IDs at the cost of reproducibility.
It is probably the second thing, but the improvement level is worth taking note of.
The paper is open access so check it out, but a TIMSTOF Pro going from 5,000 some protein groups to 7,000 protein groups (? hard to see on the bar plot? by using 10 different 1/k0 isolation settings across the gradient vs the default instrument settings? That's a surprising improvement. Worth noting that the gains aren't as impressive at shorter chromatography - you see the biggest gains at the longest relative gradients.
Downside here - like just about every TIMSTOF paper out there - I don't think that I could walk up to the TIMSTOF Pro2 in our core and reproduce this method exactly from the method as described in the paper. Thats a bigger problem for addressing later.
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