Vicinity elimination postprocessing

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Vicinity elimination postprocessing

April 21, 2012, 12:18:23 AM

I read in the often-cited Smith 2006 Analytical Chemistry paper that the vicinity elimination postprocessing step removes peaks within 0.7 m/z of the higher-intensity peaks. Is there some way to adjust that m/z range or turn that feature off when you've got better spectral resolution than that? Is that something that happens when you call xcmsSet or does it happen within some other function?

Thanks in advance!
Laura S.

Re: Vicinity elimination postprocessing

Reply #1 – April 30, 2012, 05:59:46 AM

I think this applies to the older "matchedFilter" algorithm.
Within "centWave" this value is much lower and should occur very rare.
Have a look at the manpage with:

Code: [Select]

?findPeaks.centWave

The argument mzdiff is what you are looking for.
But I'm not 100% sure, if the default -0.001 means that no peak is removed.
I will check it.

Carsten