Fengchao

It won’t help. But we will support ddaPASEF soon. Best, Fengchao

It seems that something was wrong with your LC-MS files or fasta file. Some hits: DDA ```shell [progress: 262/262 (100%) - 2278 spectra/s] 0.1s | remapping alternative proteins and postprocessing...

Thanks for uploading your files. The `*` in your fasta file broke the program ``` >PIERCE_88320 SSAAPPPPPR* GISNEGQNASIK* HVLTSIGEK* DIPVPKPK* IGDYAGIK* TASEFDSAIAQDK* SAAGAFGPELSR* ELGQSGVDTYLQTK* GLILVGGYGTR* GILFVGSGVSGGEEGAR* SFANQPLEVVYSK* LTILEELR* NGFILDGFPR* ELASGLSFPVGFK*...

You can do that with a small trick 1. Change the heavy `K` to `B` in your fasta file 2. Change the heavy `R` to `J` in your fasta file...

It is not DIA-NN, it is MSBooster @yangkl96 . Best, Fengchao

@yangkl96 Any updates about this MSBooster error? Thanks, Fengchao

Thank you so much for the testing. The error is because EasyPQP doesn't support the noncanonical amino acids. I have fixed it (https://github.com/grosenberger/easypqp/commit/17d49cd184baaf9d0581366636bfd4231d4057a5) and released a new version. Could you...

I apologize for the oversight. I should have tested it before pushing the commits. It is actually more complicated than I thought. I pushed a new commit, https://github.com/Nesvilab/easypqp/commit/83247ba8cc2bf79355325c5f0923681cb8da2b71, trying to...

Yes, I agree. It seems that using noncanonical amino acids to replace the labeled ones is not very ideal. We will discuss to see if we can implement the protein-specific...

Hi Witek, What is the "custom TMT tags"? With TMT 16, you can specify sample names for 9 of them and set `NA` for rest of 7 when editing the...