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Topic: Problems importing Bruker Files

Hello,

I've problems importing data from our new Bruker Solarix FTICR into mMass 3.8. CompaxxXport 3.0.2 is installed. There is always an error message "Unable to convert data. Make sure Bruker's CompaxxXport is installed on this computer. Importing data aquired by our old Bruker Reflex works. Any suggestions?

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Re: Problems importing Bruker Files

Hi,
- check compass installation: type "CompassXport" into comand line and press enter.
- check for any non-ascii characters in your document path
- try to drag the document folder into mMass window
- choose .baf file not fid
- in mMass preferences choose different conversion format (.mzML, .mzXML, .mzData)

martin

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Re: Problems importing Bruker Files

Hello,

I have been having a slightly different problem importing Bruker spectra.  After converting the .baf files into .mzData,.mzXML, etc. I tried to open them with mMass, and although there appear to be no errors, after ten minutes of "reading data", I still haven't opened the file.  I checked the files out with Insilicos viewer, and they appear to have converted correctly, so I don't think they are corrupted.  The instrument is a FT-ICR, and the .mzXML file is roughly 26Mb (the .mzML file is around 40Mb).  I have tried all of the file formats that CompassXport supports and multiple spectra with the same result.  Is this simply too large for mMass to handle? Is there any way to speed up the process? 

Thanks,

Owen

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Re: Problems importing Bruker Files

Hi Owen,
this is not a problem with data size (my LCMS file is about 1GB and I can still open it). Just a few questions...

- What is your mMass version?
- What is your OS?
- How many scans are you opening at once?
- Could I download your data to test it?

Best wishes,
Martin

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Re: Problems importing Bruker Files

Hi Martin,

To answer your questions:

1) I have tried with both mMass 3.8 and 3.9, and neither worked
2) I tried with Windows XP and Mac OSX 10.6.6 (I plan to use it on the mac, but I tried on the PC just to be safe)
3) The file I was trying to open was one scan in m/z domain

Also, I left it to open, and after about 15 min, it finally did, but was then moving (resizing and scrolling) very slowly.  I have a core i5 processor, so I don't think that is the problem. If you can't think of anything, I might be able to send you one of the spectra, but I'll have to check.

Thanks,

Owen

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Re: Problems importing Bruker Files

Hi,
just two more questions...

- Are you opening profile data or centroides (discrete points)?
- How many points do you have in the spectrum?

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Re: Problems importing Bruker Files

Hi Owen,

I have spent some time with your data trying various data formats and different ways of import but the result seems to be exactly what you have said before. Your data are too large. I have found that your single spectrum contains 4 millions of data points which is simply too much for both, loading and further processing in mMass. It may be because of the python "speed" or my programming "skills" as well. For such high-res data we would need to wait for better computers or I will have to start learning the C language :-)
Sorry...

Best wishes,
Martin

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Re: Problems importing Bruker Files

Hi,
I have made couple of changes in the core library of and the processing of high-resolution data will be much faster in the next mMass version. BTW, note that opening of native mMass documents is much faster than opening of other formats.

Martin

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Re: Problems importing Bruker Files

Hi Martin,

I've just tested the new version with my Bruker files, but I'm still not able to import them into mMass. I've seen that you have a Bruker FTICR in your lab. Are you able to import the data of this machine? If yes, can you explain in detail the import procedure?

Bye byte and Happy Coding

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Re: Problems importing Bruker Files

Hi,
for me it works fine (although sometimes it is very slow process).
As I've posted earlier:

- check compass installation: type "CompassXport" into comand line and press enter.
- check for any non-ascii characters in your document path
- try to drag the document folder into mMass window or choose .baf file (not fid!!!)
- in mMass preferences try to choose different conversion format (.mzML, .mzXML, .mzData)

Please note, that CompassXport is available just for MS Windows.

Martin