Summary file

[daniswan]

I would love to see a summary file that reports the samples analyzed (rows) vs. some overall statistics (columns), like psms, peptides, proteins per sample, PTM modified peptides per sample.

[anesvi]

Yes, that’s a good idea. I think MaxQuant reports something like that. We can discuss with Felipe if philosopher can generate some simple summary table.

Thanks for using our tools!

Best Alexey

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I would love to see a summary file that reports the samples analyzed (rows) vs. some overall statistics (columns), like psms, peptides, proteins per sample, PTM modified peptides per sample.

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[BenSamy2020]

Greetings @fcyu,

May I know if the enhancement will be implemented soon?

Regards, Ben

[fcyu]

Hi Ben,

To be honest, I am not sure. We are working on other modules in FragPipe to add some new functionalities. If I have time, I will add a module in IonQuant to generate summary report.

Best,

Fengchao

[BenSamy2020]

Greetings @fcyu,

You guys developed a really amazing tool. I appreciate the fact that it is consistently being maintained and updated with lots of new features. I also have established it as a pipeline for my core facility.

For the summary report, MS/MS, PSM, peptide and protein count would be sufficient.

Regards, Ben

[fcyu]

Hi Ben,

Thanks for your kind words! We will keep you posted.

Best,

Fengchao

[haianhle]

Hi @fcyu and @anesvi, is there a way to get the intensity information for each peptide associated with each run from the output files like the one MaxQuant provides in peptide.tsv? Thank you so much.

[fcyu]

You can find it from combined_peptide.tsv, combined_modified_peptide.tsv, or combined_ion.tsv.

Best,

Fengchao