Question: Thermo Xcalibur RAW data to MGF
0
gravatar for hwu12
15 months ago by
hwu1210
hwu1210 wrote:

I was wondering if there is any bioconductor package can convert the RAW file from Thermo Xcalibur to MGF file? If not, is there anything available for Mac OS? Thanks!

ADD COMMENTlink modified 15 months ago by Laurent Gatto1.2k • written 15 months ago by hwu1210
Answer: Thermo Xcalibur RAW data to MGF
2
gravatar for Laurent Gatto
15 months ago by
Laurent Gatto1.2k
Belgium
Laurent Gatto1.2k wrote:

The short answer is no, because to access (and this convert) proprietary Thermo raw data, you need to their libraries that are only available on Windows. That would mean that an R package would need to (i) incorporate these proprietary binary Thermo libraries and (ii) only be available on Windows.

You will need to use msconvert from the Proteowizard project (on Windows) to convert them to an open format such as mzML or mgf. The latter can be processed in R with MSnbase.

It is apparently possible (although I have never tried it myself) to get the Thermo libraries to run under Mono on Linux. I don't know if this would also work on OSX though.

ADD COMMENTlink written 15 months ago by Laurent Gatto1.2k
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