David Hollenstein

Dear FragPipe Team, **Is your feature request related to a problem?** The requested feature is only for convenience. Currently the psm.tsv, ion.tsv, and peptide.tsv tables (and the combined versions of...

Wrong peptide start and end positions

1

Dear FragPipe Team, First of all, thank you very much for providing these fantastic tools. I am working at a proteomics MS facility and we are planning to switch to...

Feature request: Specifying multiple fasta files

2

Dear developers, **Describe the issue or question** I found an old issue [#396](https://github.com/Nesvilab/FragPipe/issues/396) were you said that you will discuss internally if you add multiple fasta support to FragPipe. I...

Feature request: Add retention time information to ion.tsv table

5

Dear FragPipe Team, **Is your feature request related to a problem?** The request is not directly related to a problem but it would allow using the FragPipe outputs for additional...

Format error in combined_protein.tsv when MS1 quant is disabled

1

Dear developers, I've stumbled upon a small, but rather inconvenient bug when FragPipe is used without MS1 quant enabled. It appears that the combined_protein.tsv contains **more cells in the entry...

Dear FragPipe Team, **Is your feature request related to a problem?** The requested feature is only for convenience. Currently the psm.tsv, ion.tsv, and peptide.tsv tables (and the combined versions of...