SpectroNaut is a bigtime player in the present/future of proteomics for very good reasons. It's really easy to hit some buttons, wait a really really long time and then get data. You can then hit some buttons and then get to some proof that what it told you was there is actually there. You don't actually have to read anything.
But -- is the data coming out of it always correct? Could you really fine tune it if you knew what you were doing?
Of course you could! So this group took some yeast(?) and some mouse digests and mixed them together and didn't mix them together and cleverly adjusted parameters until they cleaned up false discoveries caused by sample to sample transfer. (This isn't "match between runs", I asked, they don't use that, but it does take hits identified in one run and look more cleverly at other runs. Is that what match between runs does? Yes, but that's not how they do it.)
End result? You have to read stuff about how to use SpectroNaut - but you can dramatically improve the number of false positives you have in your data, preserve your reputation, and feel smarter for having read something so practical today.
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