dnwhdals

I tried to re-load TMT10 workflow and re-run the search, but same issue was occurred. In the PSM.tsv file, no "purity" column was created during the process. Could you more...

[log_2021-09-26_01-54-25.zip](https://github.com/Nesvilab/FragPipe/files/7238404/log_2021-09-26_01-54-25.zip) Hi Fengchao. Please find the attached zip file. I can also see the free quant and label quant in a dry run console. `FreeQuant [Work dir: E:\Jacob\NPTDAB_Raw_data\AB01] E:\Jacob\fragpipe\tools\philosopher\philosopher.exe freequant...

[log_2021-09-27_13-11-48.zip](https://github.com/Nesvilab/FragPipe/files/7238516/log_2021-09-27_13-11-48.zip) Could you check out the new log file attached? I uploaded a log file that was created when I first noticed the problem, but strangely there was no labelquant...

No, there is no 'Purity' column on the psm.tsv file. Please take a look the top row of psm file. If you need psm.tsv, I can send you via email...

Hi, Sarah. I uploaded the files in the dropbox so you can take a look. The raw file I uploaded is only partial of entire dataset. We have currently 864...

Hi Alexey, Sounds good to me. I will try to rerun with marking the option of skip PSM quantification. And thank you, Fengchao, for your help! JW

hi Sarah, Sorry for your inconvenience, please double check the uploaded. You can also directly email me at [email protected] Thank you! JW

Thank you for your suggestion. The files have been searched by MaxQuant before so I believe it would work on the FragPipe. As you suggested, I will try to convert...

Agreed, Alexey.

Hi, Surendra. Recently we resolved the missing purity issue using conversion to mxML. I used[ this tool ](https://fragpipe.nesvilab.org/docs/tutorial_convert.html)to convert the files. Hope this is helpful for you. JM