MSConvertGUI - Raw files are identified as corrupted

[MAmaldacker]

Hello Phil,

I started to work with TMT lately for my Master thesis and I'm eager to introduce your well described workflow in our data analysis pipeline. The time you invested in the documentation is tremendous and at this point: Many thanks! I started to follow your workflow but faced the first problem with the MSConverterGUI. The only output I can get is an error message saying my raw files are corrupted, which they are not. I use raw files from a QExactivePlus for TMT2-based quantification and run your scripts with Anaconda 3.6.6. and MSConverter Version 3.0. Are there any incompatibilities or problems you noticed earlier in that context.

[pwilmart]

Hi, See these installation instructions for setting up MSConvert (there is a similar process for Comet): https://github.com/pwilmart/PAW_pipeline/blob/master/docs/MSConvert.md <https://github.com/pwilmart/PAW_pipeline/blob/master/docs/MSConvert.md> The script is not able to run MSConvert.exe so there is no output file for the next step to read. Cheers, Phil

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On Feb 28, 2022, at 2:06 AM, MAmaldacker ***@***.***> wrote: Hello Phil, I started to work with TMT lately for my Master thesis and I'm eager to introduce your well descirbed workflow in our data analysis pipeline. The time you invested in the documentation is tremendous and at this point: Many thanks! I started to follow your workflow but faced the first problem with the MSConverterGUI. The only output I can get is a error message saying my raw files are corrupted, which they are not. I use raw files from a QExactive for TMT2-based quantification and run your scripts with Anaconda 3.6.6. and MSConverter Version 3.0. Are there any incompatibilities or problems you noticed earlier in that context. — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFZNQSWAHTOVX4LQXCMHDSTU5NCKZANCNFSM5PQUCH5Q>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.