Identified features does not match mz values in raw files

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Identified features does not match mz values in raw files

September 25, 2014, 02:44:19 AM

My problem is that the features identified by XCMS are off with around 0.02Da compared to raw files (.d) accessed by Bruker's Data Analysis 4.2.
What could be the explanation for this?

I am using RStudio (Version 0.98.994), XCMS (version 1.38.0).

I have a HPLC-qTOF (Bruker) which produces .d files. I have converted these files into .mzXML files by CompassXport 3.0.

Following I run

Code: [Select]

library(xcms)
xset <- xcmsSet(myDir, ppm = 30, peakwidth = c(10,60), method = "centWave", snthresh = 10, noise=100, prefilter = c(4,1000), 
                mzCenterFun = "wMean", integrate = 1, mzdiff=-0.01, fitgauss = TRUE, profparam = list("step" = 0.01)) 

xset1 <- group(xset, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset2 <- retcor(xset1, missing = 1, extra = 1, smooth = "loess", span = 0.2, family = "symmetric") 
xset3 <- group(xset2, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset4 <- fillPeaks.chrom(xset3)
reporttab <- diffreport(xset4, "A", "B", "Outputfile2", 11, metlin = 0.15, h = 480, w = 640)
xset5 <- peakTable(xset4, filebase="name")

Any help is really appreciated!

Re: Identified features does not match mz values in raw file

Reply #1 – September 25, 2014, 02:54:29 AM

Check the mzXML files for example in mzMine. It might be that the files have been converted uncalibrated:

Quote

Both proteowizard’s msconvert and the CompassXport tool provided by Bruker to convert the proprietary format only export calibrated data after changing a specific windows registry key (see below). A user being unaware of this fact will obviously not be able to carry out a proper data analysis.

Suggested solutions
Update to a recent version of CompassXport and simply enable the use of calibrated data by modifying the appropriate windows registry key.
Create a file called “UseEnhancedMSMSUseRecalibratedSpectra.reg” and copy the following:
Code: [Select]
Windows Registry Editor Version 5.00 
[HKEY_LOCAL_MACHINESOFTWAREBruker DaltonikCompassXport] 
"UseEnhancedMSMS"=dword:00000001 
"UseRecalibratedSpectra"=dword:00000001 
Then execute this file. The converters should now work correctly.

ref: http://http://link.springer.com/article/10.1007/s00216-013-6954-6

Re: Identified features does not match mz values in raw file

Reply #2 – September 25, 2014, 03:30:49 AM

Thanks. I had a look at mzXML files in mzMINE and it seems to be a problem with the conversion from .d to mzXML.
I had a look in the registry key, but I can't see any wrong settings there... So I'm still lost.

Re: Identified features does not match mz values in raw file

Reply #3 – September 25, 2014, 05:09:16 AM

Some things I would try:

Newer version of CompassXport
msconvert from proteowizard

Re: Identified features does not match mz values in raw file

Reply #4 – September 25, 2014, 05:31:49 AM

I tried to export to mzXML files manually from Bruker's DataAnalysis, thereby not using CompassXport. (The disadvantage is that you can only export one file at a time, so it takes more time compared to CompassXport)

However, by doing so I fixed the problems and got the 'real' mz values after running XCMS.

So the problem is the conversion by the CompassXport program.