luizalmeida93

Hi, I am trying to use Fragpipe for TMT 6-plex and can't generate the files compatible with MSstats. I was wondering if I am doing anything wrong or if Fragpipe/Philosopher...

Hi Fengchao, Thank you for such a speedy response. I am attaching the log file. Please, let me know if you need anything else! [log_2024-02-18_13-22-23.txt](https://github.com/Nesvilab/FragPipe/files/14324321/log_2024-02-18_13-22-23.txt) Best, Luiz

I see, that's ok, at least now I know I am not doing something wrong on my end. I won't be able to use Fragpipe to generate an output of...

Hi Fengchao, I was reading the log file and noticed that DIA-NN gets triggered even though I loaded DDA files and did not enable "Spectral library generation" or "Quant (DIA)"....

I guess I found the answer to my question. I am sharing my finding with anyone who might encounter the same problem. It does seem that the formula input ends...

Hi @dcjones, thanks for developing such a cool tool! I have two questions for you, and they fit well in this thread. 1) I was wondering how the proseg_to_baysor function...

@kousaa, I used a package called SOPA (https://gustaveroussy.github.io/sopa/), which provides a convenient way of running multiple cell segmentation algorithms. The package is based on spatialdata standards, so the output is...