AlphaPept input files

[tejalal]

I found error while executing AlphaPept input file. According to the intable_config.yaml, the results_peptides.csv file should have these columns ['protein_group', 'decoy', 'ms1_int_sum', 'charge', 'shortname', 'sequence']. However, the column 'ms1_int_sum' is not present in the results_peptides.csv generated by the AlphaPept. Instead, the AlphaPept generated files has these columns 'ms1_int_sum_apex', 'ms1_int_sum_area', and 'ms1_int_sum_apex_dn'. Therefore, when we tried to execute AlphaPept generated results_peptides.csv file, the program terminates with error.

TypeError: format not specified in intable_config.yaml!

It would be helpful if it can be clarified. Also, I didnt found any sample data file/examaple for AlphaPept that can be executed with directlfq.

Lastly, I also have confusion, the results-peptides.csv file is generated in the quantification step of the AlphaPept. Can we take the required columns after the protein grouping step from the results.hdf (dataset = 'protein_fdr'). 'protein_fdr' table is saved in the results.hdf after protein grouping step.

[ammarcsj]

Hi @tejalal,

thanks a lot for the feedback! Indeed the headers should be updated to the newest AlphaPept version, seems like they applied to an older version. I updated the code now and the next release should also be compatible. In the meanwhile, you can also change the line
precursor_intensity: ms1_int_sum
to
precursor_intensity: ms1_int_sum_area

in the intable_config.yaml . This should fix the issue.

Concerning the .hdf files, so the results_peptides.csv file is already filtered for protein level FDR. This filtering should be kept, also if you extract from the .hdf directly. Does this answer the question.

Best
Constantin

[Teja-ngi]

Thank you @ammarcsj it was really helpful!