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Messages - krista

32
XCMS / centWave & ROIs
Hello,

I am hoping for some clarification on the ROIs generated by centWave and the features ultimately identified after the wavelet step. In particular, can you have one ROI that ultimately ends up being two features?

I think, from reading the Tautenhahn 2008 paper, the answer is yes (see bottom of page 7 of 16), but can someone confirm that?

Thanks,
Krista
33
XCMS / Re: centWave with LC FT-ICR MS
Paul,

Thanks for helping me think this through. I will keep working with the different converters and see what I find. I had not thought about the fact that the MSConverter might be doing a *better* job and would therefore allow me to decrease the ppm. If I lower the ppm to 2, the data insertion errors go away with the MSConverter. Since the FT should be at 1 ppm error, perhaps that is enough of a 'generous multiple' as recommended in the Tautenhahn centWave paper for this instrument.

Krista
34
XCMS / Re: centWave with LC FT-ICR MS
Sorry, forgot to answer the second question. If I leave the centWave parameters at the defaults, I get the following:

65555 peak data insertion errors for the data converted with MSConvert
0 peak data insertion errors for the data converted with ReAdW.

So, the number of peak data insertion errors increases. While the ReAdW file is not giving data insertion errors, these are the peaks I am getting:
[attachment=0:11e5y6w7]RAWpp.png[/attachment:11e5y6w7]

for plotPeaks:
xr <-xcmsRaw(mzdatafile)
> profStep(xr) <-0.05
> plotPeaks(xr,xC@peaks[1:25,])

[attachment deleted by admin]
35
XCMS / Re: centWave with LC FT-ICR MS
This is FT-ICR data, not Obitrap data.

I did in fact figure out that the error was a memory problem. However, given the figure for the CDF data, I think that it might be best if I put the XConvert/CDF aside for the moment.

Thanks,
Krista
36
XCMS / Re: centWave with LC FT-ICR MS
Hello,

I tried the CDF converter from Thermo, and that is causing new and fun errors (unrelated to the data insertion problems). When I try to run findPeaks.centWave on the CDF file, I get an error message "Error: cannot allocate vector of size 285.8 Mb" ...However, when I use the method that manually finds the ROIs (using the code you described for 'My Peaks are not picked') I get the following (quite ugly) image:
[attachment=2:3j1fku0y]cdf.png[/attachment:3j1fku0y]

For comparison...this is the figure when I try to use the ReAdW converter:
[attachment=1:3j1fku0y]raw.png[/attachment:3j1fku0y]

While this version is the one with the MSConvert tool:
[attachment=0:3j1fku0y]MSConvert.png[/attachment:3j1fku0y]

I have tested out findPeaks.matchedFilter and I get what I consider more normal looking peaks using plotPeaks. However, I am concerned about the loss of resolution because of the binning steps.

The complete error message I get when running findPeaks.centWave is 'There were [some number] peak data insertion problems. Please try lowering the "ppm" parameter' ... However, as I originally noted, whether or not this message appears varies depending on how I have converted the data to mzXML files.

I tried traceback() after getting this message, and I get 'No traceback available' ...however, I should note that I am quite new to R and I might have misunderstood.

Thanks for your help.
Krista

[attachment deleted by admin]
37
XCMS / Re: centWave with LC FT-ICR MS
Thanks for the prompt reply.

Sorry for the confusion. I was loading the data into an xcmsRaw structure first so that I could plot the peaks I found with xcmsSet using: plotPeaks(xraw,xset@peaks)

When I use the last section of code you provided for one file, I still have the data insertion errors. So, my question is really whether there are known issue with the ReAdW converter and/or the MSConverter with LC FT-MS data and the centWave algorithm? And/or is there something else  I am missing about how to use the centWave algorithm with FT data?

Krista
38
XCMS / centWave with LC FT-ICR MS
Hello,

I am trying to use the centWave algorithm to look at LC FT-ICR MS data. The data are collected on a 7 Tesla Thermo LTQ FT. I have been using two different ways to convert the data from RAW files to mzXML files: (1) ReAdW.exe and (2) MSconverter. However, I am getting different behavior with each converter, and am having downstream problems with centwave (which may or may not be related to the format conversion).

When I try to run xcmsSet with method = "centWave" with ppm of 3 on the data converted with the MSConverter, I get 722 data insertion errors, and 291 features. The ReAdW converter results in 0 data insertion errors, but also only finds 5 features. If I look at the individual scans (in Matlab), the ReAdW converter seems to have peaks heights that are too high based on what I see in XCalibur and the ReAdW converter misses peaks that are visible in XCalibur.

In reading through the Google groups forum, it seems that one of the possibilities is that the data are 'poorly centroided' so I went back and collected data in centroid and profile mode, and I still get data insertion errors with the data coming off the instrument in centroid mode (though the actual number of errors does vary). If I lower the ppm to 2, I do get rid of the data insertion errors, but that seems awfully low given the recommendation to use a higher ppm than the instrument is capable of obtaining. Also ,the features visualized using plotPeaks with the ppm = 2, are not all nice peaks since some of the peaks look like one section picked out of an apparently random section of the TIC data.

I tried implementing Tony's peakShape method (Google Groups, 12/3/2009) to remove noise peaks, but it comes back with an error and my R is not good enough to figure out where the problem lies.

Any thoughts?

xr <-xcmsRaw(mzdatafile,profmethod ="bin",profstep=0.1)

xd <- xcmsSet(xr,method = "centWave", snthresh = 10,ppm=3,prefilter = c(3,150),
  peakwidth=c(5,60),mzCenterFun="wMean",integrate = 1,fitgauss= TRUE,noise = 100)

sessionInfo() : R 2.13.1 ; xcms_1.26.1

Thanks,
Krista
40
CAMERA / isotopes - negative ion mode
Hello,

In the forum for XCMS-online, there is some discussion about the notation used to indicate isotopes in negative ion mode. My understanding  is that the output has been changed to have negative isotopes be marked as [M+1]-

However, I am using R/XCMS/CAMERA (not the online version) to identify isotopes in my samples which have been run in negative ion mode. The resulting list presents data such as: [1][M]+ ... which seems to be the 12C version of a compound that is singly-charged. Would it also be possible to change CAMERA to match the output of xcms online (which is far more intuitive for negative ion mode)?

Thanks,
Krista
41
XCMS / searchMetlin
Hello,

I am currently learning how to use R and xcms, and am quite impressed with what I have found so far. One feature that appears to be in xcms-online has been causing me some problems in xcms; that feature is 'searchMetlin' (and the related 'simSearch'). I find notes and references for searchMetlin, but the functionality seems to be offline at the moment. I see in the old Google forum this was listed as offline in Jan 2011. Is there any plan to return this function to xcms any time soon?

Thanks,
Krista