Re: Spectra versus XCMS/Camera
Reply #1 –
Are you talking about which m/z value to use? The one from the peaktable or from the raw data?
In xcms the m/z for each feature in individual samples is the intensity weighted mean across the peak. Then when you group features across samples it uses the median m/z of those mean values.
Because of this averaging the m/z in your peaktable should have a bit better accuracy. That is under the assumption that the parameters were sane enough not to group things that are NOT the same compound. So using this value you should normally be able to restrict your m/z range more when you search.