Request of examples of how to use the functions in matching.py (Match between Run)

[grimace9527]

Dear AlphaPept Team,

I find this toolkit useful when dealing with MS data, thanks.

Is your feature request related to a problem? Please describe.
The wiki page https://mannlabs.github.io/alphapept/matching.html provides many user-friendly usage of different functions. Could you please give more examples, such as the retention time alignment functions in the file matching.py.

Describe the solution you'd like
Could you please tell me which format of data I should provide when I want to perform retention time alignment between two or more data results, like the example you give under delayed_normalization() function (https://mannlabs.github.io/alphapept/quantification.html#delayed-normalization-1)? Since sometimes I'd like to do the alignment job based on results of other software like MaxQuant, I think it will be much helpful to show the format of dataframe to input.

Describe alternatives you've considered

Additional context
Thanks again for your reply!
: )

[straussmaximilian]

Hi grimace9527,
Thanks for your interest.
Could you tell us a bit more about the use-case?

• For Matching: Do you have access to MS1 features (e.g. from MaxQuant)? As only MS2 identifications will be tricky for alignment

If you have some example files I probably could compile an example notebook..

[grimace9527]

Hi Dr. Strauss,
Thank you very much for your reply.

I have access to MS1 features from MaxQuant ("combined\txt\allPeptides.txt" in MaxQuant result folder) with messages in these columns: (screenshot from "tables.pdf" of MaxQuant result, a file explaining the information in each columns)

The "Sequence" column of each row does not always contain a value, since not all precursors are fragmented in MS2, and the values present represent search results.

If detailed results are needed, I will upload these files afterwards.
If anything else is also needed, please tell me and I will prepare it.

Thanks again for your kind help! : )