Finding PTMs in complex proteomics data is either
A) very focused (looking for 1 or 2 PTMs and taking a minor hit in false discovery rate calculations
B) Not focused at all (open searching) and taking a big 'ol hit in your false discovery rate maths
Obviously we've got really cool tools today to help with B). We can recalibrate our MS1 and MS2 spectra to accuracy levels beyond what the instruments are capable of themselves. And we can hunt for diagnostic fragment ions and we can start to adjust our retention time predictions and on and on.
MGVB is a neat new approach that could be integrated into helping make B even better.
I'm going to call it simple because even I can follow the math in re-evaluating the fragmentation spectrum delta masses.
And it seems to help in 3 or 4 validation datasets the author pulled from repositories and applied this to.
While I can't apply this myself, I can draw some attention to it and - this Github (https://github.com/mvm1964/MGVB) - and maybe it'll end up making tools that I use a little better?
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