Error for running mzData files converted using Mascot

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Error for running mzData files converted using Mascot

September 13, 2013, 12:19:17 PM

I processed the Agilent .d folder files to get the peak lists that were then saved into files in the mzData format using Mascot Distiller. Unfortunately, xcms process stopped after I ran "xset <- xcmsSet(myfiles)". The error message is "Error in if (yfilt[maxy] > 0 && yfilt[maxy] > snthresh * noise && ysums[maxy] > : missing value where TRUE/FALSE needed". Is there anyone who had similar situation and got this kind of error before? Thanks.

Jeff

Re: Error for running mzData files converted using Mascot

Reply #1 – September 15, 2013, 03:45:36 PM

Jeff,

Agilent has their own data converted to mzData. It's been a really long time since I played with any Agilent MSs but It should still be hiding under MassHunter under one of the tabs about processing (I think). Otherwise you could use MSconvert from ProteoWizard: https://xcmsonline.scripps.edu/docs/fileformats.html.

As for using Mascot Distiller, it's been an even longer time since I looked at it in any detail but I believe it does a peak detection on the file so that the resulting mzData or file X is peak picked MS1 and then full MS/MS scans related to those peaks. Unfortunately, just because it's an mzData format does not mean that it has the required data in the file for xcms to process .

Hope it helps, let us know how you get on.

Paul

Re: Error for running mzData files converted using Mascot

Reply #2 – September 16, 2013, 08:30:57 AM

Hi Paul,

I greatly appreciate your answers. You are right, Agilent's MassHunter software the conversion function (from d. fold to mzdata.xml). But the file size is quite big (~150-200M per file). When I tried to use Mascot Distiller, it gave me mzData files with size less than 10M. Unfortunately, the Mascot Distiller-converted files could not be used for XCMS analysis. Very likely, the file conversion in this way loses so many details that XCMS cannot process them.

Now I try to use MSconverter (from ProteoWizard) for file conversion. The resulting mzXML files are a little bit smaller than the ones from MassHunter. I am employing XCMS to process these files. I will keep you informed of progress.

Jeff

Re: Error for running mzData files converted using Mascot

Reply #3 – September 18, 2013, 03:15:24 PM

It is fine now for me to use XCMS to process and analyze the mzXML files that were converted from Agilent's d. folders by MSConverter. I can get corrected EIC graphs and txt file listing the peaks, p values, Metlin database links, intensities and other information. Thanks for your help.

Best wishes,

Jeff