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Error attempting to parse Chromoleon7 raw files #160
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Hi @hnnsmchls, thank you for your interest in ThermoRawFileParser. Personally, I only work with LC-MS data from Thermo instruments (proteomics, metabolomics, to be precise). TRFP and supported formats are centered around MS data. If your file does not contain any MS, i.e. it has only chromatography data, TRFP cannot process it currently. A recent pull request (#157) aims to solve this issue, however, I didn't have a chance to check and release it yet, but the updated version can be compiled from the source. The file you have provided seems to be corrupted - that is the usual cause of the error you face, I could not open it in QualBrowser or Freestyle as well. Did you try to use any other files from the same instrument? Regarding the "simpler" format, you can try Parquet output, it can be read by pandas. Another option is this tool that can produce CSV output, but only from MS data, no chromatograms. Finally, you can see the script in #133 and #134 to convert chromatograms or spectra stored in mzML to DataFrames. I hope that helps, but feel free to ask any further questions. |
Hi @caetera, |
The pull request should allow processing files that contain only chromatography data, it will still produce (for example) an mzML file with chromatograms, but no spectra, thus, I believe you might give it a try for pure GC data. |
Hi caetera, |
Hi @hnnsmchls , I am not very familiar with the Mono setup on Windows, on other platforms you just need to clone (or download) the repository and then use Mono's Another option to compile from the source on Windows is to set Visual Studio (it is free for personal use and you only need C#) and next open the solution file |
The new version (1.4.3) adds support for MS-less RAW files. Please, see if it is something that helps in your case. |
Hello,
I am extremely glad I found this tool. I am attempting to parse raw files from our Trace1310 Thermofisher gas chromatograph, I intend to implement this on an automated basis within a python routine later. However, already trying out a single conversion with the GUI gives the following error:
I appreciate any help and guidance.
The raw file can be found here: https://ufile.io/k0paibr1
P.S.: Tips on which settings to use for most simple output to file formats that can be read by pandas/.. are also welcome!
Kind regards,
H
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