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Topic: MRM data? (Read 5358 times) previous topic - next topic

  • nvinayav
  • [*]
MRM data?
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.

  • Ralf
  • [*][*][*][*]
Re: MRM data?
Reply #1
Sorry, MRM data analysis is not supported by XCMS, yet.
Volunteers are welcome :)

  • sneumann
  • [*][*][*]
Re: MRM data?
Reply #2
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
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

  • nvinayav
  • [*]
Re: MRM data?
Reply #3
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

  • bowenli37
  • [*]
Re: MRM data?
Reply #4
Hi Steffen,

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

Li Bowen

  • sneumann
  • [*][*][*]
Re: MRM data?
Reply #5
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.
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

  • bowenli37
  • [*]
Re: MRM data?
Reply #6
Hi Steffen,

An example MRM mzxml file is attached.

Regards,
Bowen

  • cbroeckl
  • [*][*]
Re: MRM data?
Reply #7
Hello XCMSers -
Just wanted to see whether there is anyone out there who has thus far figured out XCMS for MRM data.  Thanks,
Corey

  • drinehart
  • [*]
Re: MRM data?
Reply #8
Please try xcmsonline-mrm.scripps.edu.  Your XCMS Online account should provide access.

Duane Rinehart
TSRI