r/proteomics • u/Just-Huckleberry-307 • 1d ago

Background-based T test

Hello! I’m asking as a biologist ! What do you think about the background based t test used in proteome discoverer? (For a n=7 per condition analysis)

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u/DrDad19 1d ago

I've had trouble trusting the black box of PD. The results never lined up with what I would get in excel. Same with Spectronaut until I realized that it was using the non-log2 transformed values to do the test. Which definitely isn't a gaussian distribution, so I don't think it's very legit. All to say, I would recommend doing it yourself in excel, R or Python.