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ProteoWizard / pwiz

The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
http://proteowizard.sourceforge.net/
Apache License 2.0
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Conversion from Bruker MS Imaging .d format (mcf, mcf_idx) #1149

Open fgrelard opened 4 years ago

fgrelard commented 4 years ago

Currently, it is not possible to convert Mass Spectrometry Imaging data obtained directly from a Bruker MALDI-TOF instrument. First, one has to export the data to multiple fid subdirectories through FlexImaging, and then use msconvert to get mzML files and eventually an imzML image.

The original exported format contains MCF and MCF_IDX files. I tried searching for documentation online but came up empty. One example can be found online => here.

The original files are:

There are no u2 or baf files, the authors in the link must have obtained them through FlexImaging.

Is the export to mzML something that you considered adding to pwiz? If you have any pointers as to how to proceed, I'll be happy to look at it myself.

chambm commented 3 years ago

The example you linked to above does have a 1.2GB analysis.baf file. That's where the data is. The MCF files are some kind of metadata.

fgrelard commented 3 years ago

An imaging example is available here. The data is stored in MCF files. See Kidney_30min -> .d subfolder.

chambm commented 3 years ago

Those datasets do have some big mcf files, but I'm not totally convinced that's where the data is. Looking at them in a hex editor I can't discern any obvious data arrays of floats or doubles.

fgrelard commented 3 years ago

Thanks for looking at this issue. I will check whether this data is sufficient for the full conversion to XMASS fid through the proprietary software. Unfortunately, I won't have access to the software in the near future. I will get back to you as soon as I can.

fgrelard commented 3 years ago

I went back to this issue. I proceeded in the following way:

  1. Isolate the .d directory, and move it to another location on the hard-drive.
  2. Open the .ddirectory in Bruker's flexDataConverter.

The file conversion works normally. I don't think files in the .ddirectory reference other files on the hard-drive because only this directory is created when starting a new acquisition.

So the .d directory seems sufficient for the conversion of the dataset.

In the example above, I am assuming the data is located in the 1.4Gb file.

chambm commented 3 years ago

I didn't mean to imply the .d directory referenced files anywhere else. Only that some files might be missing from it. If you find any SDK that can read this data, we can integrate it to read the files directly, but your conversion using Bruker's converter to fid (BAF would be better if you can do that) may be your only option now.