Fengchao comments

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                                            Fengchao

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

Hi David, Thank you very much for the explanation of using `ion.tsv` over `combined_ion.tsv`. For now, I would stick to the `combined_ion.tsv` due to the limited bandwidth. > When we...

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

Implemented it. Email yufeATumich.edu (replace `AT` with `@`) if you want to test the pre-released version. Best, Fengchao

Saved settings on FragPipe-PDV

Hi Tobi, You are correct. The PDV settings are not saved to FragPipe cache. I will discuss with @KaiLiCn to implement it. Best, Fengchao

IonQuant error in TMT16 workflow with Thermo raw but not mzml

Hi Todd, Thanks for the bug reporting. I guess IonQuant had some issue when extracting certain information from the raw file. Could you upload `2023Dec_37_F1.raw` to https://www.dropbox.com/request/com7mlVE2vQB5J5hONBA ? I will...

IonQuant error in TMT16 workflow with Thermo raw but not mzml

Thanks for your raw file. The parent scan number information is not available in the raw file. I have fix this bug. If you want to test the fixed version,...

IonQuant error in TMT16 workflow with Thermo raw but not mzml

Thank you for the feedback. We have fixed it and the next release will be available in a few days. Best, Fengchao

IonQuant error in TMT16 workflow with Thermo raw but not mzml

Fixed in the latest version. Best, Fengchao

MSFragger-DIA for Bruker TimsTOF files

Yes, we are working on it. Best, Fengchao

MSFragger-DIA for Bruker TimsTOF files

We have released a new tool diaTracer that can generate pseudo-MS/MS for diaPASEF data. Coupled with FragPipe, you can analyze the diaPASEF data without any ddaPASED data as library. Please...

Got trouble when using two_pass_search of Fragpipe

It currently doesn't support ddaPASEF .d files: https://github.com/Nesvilab/FragPipe/issues/1417 Best, Fengchao