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Topic: Problem with opening Bruker Files

Hi Martin,
I am trying to open my Bruker FTICRMS file using your program. I have version 5.4.1 of the mMass software. I am using a Windows 7 computer. I have so far been unable to open either the analysis.baf file or the fid file. I think the problem is with the Compass Xport software, as when I try and convert the files using it, I keep getting an error (ID 120). I am not sure if I am entering the file correctly either which could be the cause. I copied/pasted both the fid and analysis.baf files into the CompassXport folder. I type the following into command: CompassXport -a analysis.baf or CompassXport -a fid. They both get that same error. I also tried entering: CompassXport -a E:/foldername/analysis.baf entering the location of the files original location.

When I try to directly open the files in mMass, the fid file does nto work at all and comes back saying it cannot open the file. The analysis.baf file does seem to convert the file to the mzML and mzXML file formats but then spends a long time trying to open the file and eventually the software has an error and closes.

Please let me know if you have any suggestions.

Thanks
Gina

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Re: Problem with opening Bruker Files

Hi Gina,
there are several things related to your problem:

1) As far as I know the fid file contains "frequencies" only, not the spectrum. Therefore this file cannot be directly converted into mzML. This is the case for FTICR. For TOF or TOF/TOF instruments it contains "intensities" only. For FTICR always use the baf file.

2) I am not sure but I assume that some other files from the spectrum directory are necessary for conversion, so you cannot just copy the baf file and convert it. Always use the full path. In addition be sure not to use any non-ascii character in the folder names.

3) It seems that by using mMass you are able to correctly convert your data.

4) FTICR data (if stored in profile mode) can easily became very huge due to its ultra-high resolution. Therefore it really takes long time to import this data into mMass. Good news is that once loaded and stored in mMass's format loading time is than better.

5) Depending on your computer performance and especially the amount of RAM it might happen that mMass is unable to load your spectrum. Increasing the amount of RAM could help.

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Re: Problem with opening Bruker Files

Hi Martin,

Thank you for your rapid response. The file size will be huge since it is 100 scans and there are several thousand peaks. I will give it a try with a different computer that has more RAM to see if I can get it to open. If I have any more issues I will let you know,

Thanks
Gina