Thursday, December 26, 2019

PeakOnly -- Deep learning Python code for finding your MS1 features!

There are a lot of ways to find compound peaks in your data, but some compounds/peptides (particularly modified ones) just have lousy elution profiles. Sometimes you just have to go in and look yourself. Isn't that what all this AI/Machine Learning/Deep learning baloney is supposed to be doing for us? Automating tasks that are a little bit harder?

Maybe this is gonna help!?!?

PeakOnly uses Deep Learning to classify peaks. It is meant for metabolomics and was optimized on 1-3 Hz MS1 data, but I'm still putting it here because there is a very short list of things that will make lists of your MS1 peaks and their abundances (quantifying the stuff you didn't identify) and I'll probably need this sooner rather than later.

You can get PeakOnly at this Github. It doesn't blow the traditional peak detection stuff away or anything, but it does identify some compounds here and there that XCMS misses. It makes for a solid proof of concept study with open (with MIT license?) code that deserves a look. I mean...I'm not having trouble with the high abundance ones with the perfectly gaussian distributions...I need help identifying the lousy ones....


  1. Interesting paper certainly. Scalability and generalizability of the model can be greatly improved.

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