Fengchao

Adjust `I` and `L` in the psm.tsv, peptide.tsv, and ion.tsv after razor assignment

11

The razor assignment might make an alternative protein as the razor protein. Since we don't distinguish `I` and `L` in the protein mapping, some peptides might not exist in their...

It is from a FragPipe user: https://github.com/Nesvilab/FragPipe/issues/1519 Thanks, Fengchao

Add a `scan number` term

8

### Describe the new term or terms you would like to add. For a long time, several search engines, including MSFragger and Comet (correct me if I am wrong), use...

This is PR revised the SDRF module based on Yasset's suggestion and feedback. No need for others to review. I will merge after thorough testing. Best, Fengchao

I always feels annoying and redundant that ProteinProphet prints the warning such as `WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6Y8|S23IP_HUUAN : UUUUUUUUUUUUUUUUUUU`. When I tested using U...

As far as I can tell currently, need to bind the directories of the LC-MS files. Do not merge it until it is fully implemented and tested. Thanks, Fengchao

Adding the contam_ prefix doesn't work with an existing database. It only works when downloading the database using Philosopher

15

This is a bug reported by emails. I put it here in case we forget it. It also let potential affected users know: human contaminant proteins are always not marked...

The `Extended Peptide` for peptide `LTDGFMLPDPQNISLR` should be `DSTIVYYK.LTDGFMLPDPQNISLR.R` not `DSTIVYYK.LTDGFMLPDPQNISLR.`  The above screenshot contains the information about the dataset. I used the `TMT10-phospho-bridge` workflow. Thanks, Fengchao