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Topic: ppm in XCMS centWave (Read 693 times) previous topic - next topic

ppm in XCMS centWave

The centWave paper says the following:
1. Mass deviation μ in ppm, typically set to a generous multiple of the mass accuracy of the mass spectrometer. We use μ = 30 ppm for the Bruker MicrOTOF-Q, which is advertised with a mass accuracy of 3–5 ppm.

But I see others use ppm=2.5, instead of 25, for Orbitrap with advertised mass accuracy < 5 ppm. Could anyone explain why?


Re: ppm in XCMS centWave

Reply #1
I would say that 2.5 is almost certainly a bad idea... It needs to be true also for the edges of peaks to work well.
I used 20 for orbitrap data and I remember that setting it significantly lower gave problems.

Re: ppm in XCMS centWave

Reply #2
Thank you so much for the reply! And thank you for all the tutorials on your page! It's very helpful for a newcomer to this field.

Here is a slide from a tutorial by Workflow4Metabolomics. Seems for Q-TOF instruments, the ppm is set to be ~10 times of actually accuracy, but not for Orbitrap. I also see others using ppm=2.5 for Orbitrap, so I was just wondering why?