how to pick peaks on a selected RT range ?

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how to pick peaks on a selected RT range ?

June 20, 2012, 09:41:31 AM

Hi to all,

I would like to know if there is a method to pick peaks only on a selected RT range with xcms.
for example on LC-MS data for a specific study, only ions eluted between the beginning of the chromatography and about 12 minutes (~720 sec) are relevant for me while retention times go until 20 minutes.
is there an particular option to do that ? something like the "scanrange" option of the centwave method but that could work on matchedFilter as well as on centwave ?

thanks for your help.

Re: how to pick peaks on a selected RT range ?

Reply #1 – June 20, 2012, 05:10:12 PM

Thanks to the mzR interface, XCMS now also supports the scanrange parameter for xcmsRaw() and xcmsSet().

Re: how to pick peaks on a selected RT range ?

Reply #2 – June 21, 2012, 04:51:22 AM

thank you for your reply Ralf.
I think I need to upgrade to the last version of xcms but my question was about selecting an RT range. Is it also possible on xcmsSet ?
I will try after upgrading.

thanks

Re: how to pick peaks on a selected RT range ?

Reply #3 – June 21, 2012, 06:30:09 AM

Until now only the scanrange can be used, so you need to convert.
If you want to check the selected scanrange you can access the scan times with:

Code: [Select]

#get scan time for scanrange = c(100,150)
xr <- xcmsRaw(filename)
xr@scantime[c(100,150)]

Re: how to pick peaks on a selected RT range ?

Reply #4 – June 22, 2012, 07:09:50 AM

thanks Carsten.
On a single file it is quite easy to select time range but using xcmsSet to upload multiple files it seems to be more difficult : I don't have the "scanrange" item but the "rt" one divided on several sub-items corresponding to each chromatogram.
I was used to handle S3 object on R and S4 ones are a bit more difficults to manipulate.