Error attempting to parse Chromoleon7 raw files

[hnnsmchls]

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

[caetera]

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.

[hnnsmchls]

Hi @caetera,
thank you very much for your valuable input.
I realised as I was going through the code that it was centered around MS data rather than gas chromatography. The pull request you showed seems to be targeting mass spectra as well...
Thank you for hinting how pandas could potentially be utilised later in the process. I will see how to get my gas chromotograph raw files read to a point where pandas can come in.
Thank you very much anyway!
H

[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.

[hnnsmchls]

Hi caetera,
thank you for having a look at this again. I did download the pull request #157, and I am attempting to run it on an example GC-raw file, however I am having trouble getting things set up on my Windows-mono prompt:
After cd to the directory of the pull request files, according to the usage instructions, with or without the 'mono':


gives this error:

which does make sense given I do not see any '.exe' file in the folder.. what am I doing wrong?
Thank you very much for the help!
H

[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 msbuild from the root of the downloaded folder (run msbuild without any parameters) - that should by default create the binary in bin\x64\Debug subfolder. The binary (I guess) could be executed as native (i.e. no mono in front), once you are on Windows.

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 ThermoRawFileParser.sln and just build it. Since you already have Mono the first option is, likely, easier.

[caetera]

The new version (1.4.3) adds support for MS-less RAW files. Please, see if it is something that helps in your case.