You know those low mass fragment ions your search engine is probably set to ignore - because - let's face it - how useful is it to know there is a protonated lysine fragment there?
We recalibrate all our TOF TMT spectra using the reporter ion exact masses using a lousy program I pulled together, but it is very manual and - not useful for something that isn't TMT.
This is dynamic and - while it has the dreaded "pip" in this Github, that's something ChatGPT can help you with if you're not sure where to get started.
I presume for Orbitrap spectra you could start talking about ppB mass accuracy after running it through something like this! For me, I just want Orbitrap level accuracy at (affordable) TOF speeds.
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