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We should be able to retain all CV params and their values found in mzML files when files are imported to MSDK and then exported again to mzML.
Example:
```
```
This is not a high-priority issue, b…
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As already described [here](https://github.com/compomics/ThermoRawFileParser/issues/112), the new version of ThermoRawFileParser creates a CVTerm in its `mzml` files
```xml
```
which is not reco…
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With the fear of repeating what has already been posted as issues. I have an issue opening pepXML+mzML and/or tsv+mzML files generated using FragPipev14.0, using Fragger 3.1.1, Philosopher 3.4.13 (bui…
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I used a recent PhenoMeNal installation, data of MTBLS36 was downloaded with
Metabolights downloader "Import public and private MetaboLights studies (Galaxy Version 3.1.0)" `mtbls-dwnld&version=3.1.0…
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Hi again!
We tested DIANN 1.8 (by command line in linux) with the same file and observed different results depending on if we used .mzML or .raw files. For instance, this is the number of precurso…
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I was running spectramerge and I found this error that lead to no output file being created. It looks like an unhandled cvParam stopped the writing of the output file. This file worked on the smoot…
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Hi, I have installed Param-medic and it works great on most of the example mzML files at:
https://noble.gs.washington.edu/proj/param-medic/
I get what appears to be good output for 9 of the 11 mzML …
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A suggestion to add the ability to generate mzIdentML reports through the FragPipe interface.
Issue with Philosopher:
Unsuccessful in using Philosopher with the pipeline mode to generate mzID file…
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**Describe the question or problem**
Error: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 when opening mzML file
I met this error report when using MS-GF+ for .mzML. I tested about 1000 .mz…
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### Basic information
* My operating system and version: Windows 10 Pro Education 22H2, OS Build 19045.4355
* My mzmine version: 4.0.8.
### What happened
I am processing approx. 1300 mzml fi…