Metabolomics Society Forum

Software => R => XCMS => Topic started by: nvinayav on September 29, 2011, 04:14:45 PM

Title: MRM data?
Post by: nvinayav on September 29, 2011, 04:14:45 PM
I have generated some MRM data from Agilent QQQ LC/MS.  I thought it would be useful to get the peak area for all of the peaks at once.  Is MRM data supported by xcms?  I have tried to use xcmsSet(), but it gave me the following messages:

> xs <- xcmsSet()
2_110927pos_wc-ptc1a: Error in seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *  :
  invalid (to - from)/by in seq(.)
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
> traceback()
11: stop("invalid (to - from)/by in seq(.)")
10: seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *
        step, by = step)
9: seq(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * step,
      by = step)
8: .local(object, ...)
7: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
6: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
5: do.call(method, list(object, ...))
4: .local(object, ...)
3: findPeaks(lcraw, ...)
2: findPeaks(lcraw, ...)
1: xcmsSet()

I guess this is understandable, since the files contain mainly MS2 data, and not MS1.  Is there any way around this problem using xcmsSet()? 

Thank you very much.
Title: Re: MRM data?
Post by: Ralf on October 06, 2011, 05:19:28 PM
Sorry, MRM data analysis is not supported by XCMS, yet.
Volunteers are welcome :)
Title: Re: MRM data?
Post by: sneumann on October 07, 2011, 01:23:42 AM
Hi nvinayav,

If you (or someone near you) has some deeper experience with R,
we could talk you through implementing this. I would need to look
how MRM is represented in these mzData (or mzML) files,
and then massage that into something that "looks" like MS1
so that the peak pickers can have a go at it. We have some experience
getting UV data into XCMS, so it is not heavy lifting, but still
not for an inexperienced R user. Are you interested ?

Yours,
Steffen
Title: Re: MRM data?
Post by: nvinayav on October 11, 2011, 04:17:30 PM
Steffen,

Thank you for your reply.  Unfortunately, I don't have any experience with R.  I will look into finding other people around here who might know R better.  I will try to contact you back when I can find someone.  Thank you.

Yui
Title: Re: MRM data?
Post by: bowenli37 on March 27, 2012, 10:43:11 PM
Hi Steffen,

I am interested in implementing MRM data support in XCMS, if it is not yet done.

Li Bowen
Title: Re: MRM data?
Post by: sneumann on March 28, 2012, 02:03:44 AM
Hi,

this is great, and I am more than happy to help you as best as I can.
So for MRM we'd first need to find out how to read the raw data
into xcmsRaw, and then verify that centWave (or matchedFilter)
can process it.

1) What format does MRM data come in ? Of course mzData/mzXML/mzML are preferred.
Can we haven an example ?

2) I am happy to put a few trimmed down raw files into the msdata package,
so that you can create manpages and a vignette around it.

Yours,
Steffen

P.S.: Depending on your preferences, we can also take the discussion
to the xcms-devel list. As you wish.
Title: Re: MRM data?
Post by: bowenli37 on April 25, 2012, 12:09:01 AM
Hi Steffen,

An example MRM mzxml file is attached.

Regards,
Bowen

[attachment deleted by admin]
Title: Re: MRM data?
Post by: cbroeckl on January 06, 2015, 01:05:55 PM
Hello XCMSers -
Just wanted to see whether there is anyone out there who has thus far figured out XCMS for MRM data.  Thanks,
Corey
Title: Re: MRM data?
Post by: drinehart on February 01, 2018, 05:11:36 PM
Please try xcmsonline-mrm.scripps.edu.  Your XCMS Online account should provide access.

Duane Rinehart
TSRI