XCMS and fast polarity switching

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XCMS and fast polarity switching

December 02, 2011, 01:00:20 AM

I am about to start a project and I will be collecting data from Q-TOF on fast polarity switching mode. When using XCMS will I need to extract and analysis positive and negative data separately, or is there code that I can apply to do the analysis as a single with both positive and negative?

Cheers
M

Re: XCMS and fast polarity switching

Reply #1 – December 02, 2011, 01:55:13 AM

Hi,

The current XCMS allows you to read in you mzData/mzXML/mzML
with alternating polarity, then you'd use split() to create two separate
pos/neg mode xcmsRaw's, and findPeaks() on them individually.
What's currently not supported out of the box is to create two pos/neg xcmsSet's
from a directory of files, but we can talk you through creating that
from the individual peak lists.

Yours,
Steffen

P.S.: I've heard many complaints that (even fast) polarity switching will reduce
the sensitivity of your measurements. I'd love to hear your
experience, e.g. if you compare the peaks detected in a purely
positive mode measurement vs. the extracted data from switching.
If you could give me access to some raw data (any non-secret data will do,
even "only" QA mix or whatever), I'd love to have a quick glance.

Re: XCMS and fast polarity switching

Reply #2 – February 17, 2012, 06:42:07 AM

With the latest xcms it should be possible to use the polarity parameter in the xcmsSet function to select only the scans from one polarity mode.
For example xcmsSet(...., polarity="positive")

Carsten

Re: XCMS and fast polarity switching

Reply #3 – December 02, 2013, 09:36:59 AM

Hi?
i have data with fast polarity switching mode from Thermo Exactive and Q-exactive,first i converted in proteowizard using pickpeaking filter( for centroid data), the i try to process the data with' polarity="positive"and" negative",but it seems the result is the same. here is the scrips:

Code: [Select]

XMLfiles=list.files(path=".", recursive=TRUE, pat="mzXML")
> 
> xset1=xcmsSet(XMLfiles, method='centWave', ppm=5, peakwidth=c(5,12), snthresh=5, polarity="positive")
xset1=group(xset1)
xset1=fillPeaks(xset1)

xset2=xcmsSet(XMLfiles, method='centWave', ppm=5, peakwidth=c(5,12), snthresh=5, polarity="negative")
xset2=group(xset2)
xset2=fillPeaks(xset2)

but xset1 and xset2 show exactly the same result. matchedfilter was also used on data without peakpicking in proteowizard , but it also showed no difference between 'polarity="negative"and "positive" '
and it's the latest version of xcms. Seek for help!
If this method not work, how to use split() ? what is the parameters?
Thanks
yaoyao