Excluding every other scan?

February 03, 2012, 03:47:08 PM

Hi:

I am trying XCMS online and although everything seems to be working, I believe there may be a problem. The issue is that my data was acquired on a Thermo LTQ-FT, thus I have two kinds of MS1 scans, with one scan in the iontrap, and one scan in the FT cell. Is it possible to have XCMS online just process one type of data at a time? For example, just the odd or even scans?

Alternatively, can one of the mzXML converters do this? Neither Proteowizard or Readw seem to have this function.

Thanks,

-Chris
crath@ucsd.edu

Re: Excluding every other scan?

Reply #1 – February 04, 2012, 02:28:01 PM

Hi Chris,

there is split() for xcmsRaw objects. Check out ?split.xcmsRaw for the documentation.
Basically, you create a vector that is as long as you xcmsRaw has scans,
and two values for the LTQ and Orbi scans. You will retrieve a list of two
xcmsRaw with only one kind of scans.

Then you can write.cdf or write.mzdata to bring these xcmsRaws back to disk,
to read them back in with xcmsSet().

HTH,
yours,
Steffen