[FEATURE] Export matched fragment ions for rescoring & spectral library generation

[grosenberger-bruker]

Hi @lazear,

For some downstream applications (spectral library generation or rescoring), algorithms require access to the scored spectra again. Most frequently, this is implemented by raw data access followed by repeat annotation of fragment ions using the PSMs. However, there is of course considerable overhead in this regard.

We thus think that it would be great if Sage natively had an option to directly export matched fragment ions based on the PSMs. This PR introduces an additional parameter that will export a parquet file containing all matched fragment ions for each PSM. Downstream applications like MS2Rescore or EasyPQP can then use the Sage PSM parquet and this new matched fragments parquet for rescoring or spectral library generation.

This is a draft PR, where we hope to receive feedback of any kind (style, implementation, algorithm, variable naming, etc.) to eventually make this feature as native as possible to Sage.

Thanks for your feedback!

[vijay-gnanasambandan-bruker]

Thank you for providing valuable feedback. I have made the necessary updates to the code based on your suggestions. Please review it again and let me know if there are any further adjustments that need to be addressed. Thank you.

[lazear]

Thanks for making changes - I will start reviewing and testing this week!

[vijay-gnanasambandan-bruker]

@lazear Thank you for approving the modifications.

[lazear]

Thank you for the excellent contribution!