ppm in XCMS centWave March 27, 2018, 09:24:24 AM Hi, The centWave paper says the following:Quote1. 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?Thanks!
Re: ppm in XCMS centWave Reply #1 – March 28, 2018, 05:48:51 AM 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 – March 28, 2018, 09:42:39 AM 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? Last Edit: March 28, 2018, 09:49:48 AM by blueskypie
Topic: ppm in XCMS centWave