Problem using quantms outputs with ibaqpy

Hi, I have used quantms to process a small proteomics experiment.
`nextflow run bigbio/quantms -r dev -profile singularity --input data/processed/run2/sdrf.tsv --database data/external/combined_proteome.fasta --outdir data/processed/run2/`

I would like to use ibaqpy to estimate the absolute quantification of the proteins. However, to run 'quantmsioc convert-diann', 'ibaqpyc features2peptides', and 'ibaqpyc peptides2protein' I need to do some processing of various files. I have attached the command line outputs, and the python scripts I used to process the files.

Specifically, I need to:
1. Remove sequences containing 'X' from diann_report.tsv.
2. Rename the column 'precursor_mz' to 'observed_mz' for all parquet files in the mzmlstatistics folder.
3. After running quantmsioc convert-diann, I need to explode the intensities column in the feature.parquet file.

Please let me know if I am using the wrong input files, or how to streamline the process going from quantms outputs to ibaqpyc peptides2protein outputs.

Many thanks,
Mathias

[ibaqpy_terminal_and_output.pdf](https://github.com/user-attachments/files/20934885/ibaqpy_terminal_and_output.pdf)
[absolute_prot_quant.pdf](https://github.com/user-attachments/files/20935019/absolute_prot_quant.pdf)

Review the attached Python scripts and command outputs alongside diann_report.tsv, the mzmlstatistics parquet files, and feature.parquet. Start by tracing the quantmsioc convert-diann, ibaqpyc features2peptides, and ibaqpyc peptides2protein inputs. Done means establishing a supported conversion path from quantms outputs or documenting which input processing is required.

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