treponeme

Hello I have noticed one other issue with the data in this conversation (same zipped log file as above: https://github.com/Nesvilab/FragPipe/files/7419927/log_2021-07-30_07-16-48.zip): Many proteins that were detected at high probabilities (>0.95) in...

?Hi Felipe Yes, this was a label-free experiment consisting of three separate samples. Thanks ________________________________ From: Felipe da Veiga Leprevost ***@***.***> Sent: November 4, 2021 12:00 PM To: Nesvilab/FragPipe Cc:...

Hello Fengchao The analyses have been re-run using the latest software, but the issues still persist. I have attached the fasta file database used for searching here. Thanks. [Tp_Cust_Rab_Crap.zip](https://github.com/Nesvilab/FragPipe/files/7488060/Tp_Cust_Rab_Crap.zip)

?Hi Here are the output tables. I will send the psm files separately. Thanks ----------------------------------------------------------- Simon Houston Ph.D. Research Associate Department of Biochemistry and Microbiology University of Victoria British Columbia...

Hi Here are the output tables. Thanks [Output_tables samples 256 257 258 and Combined.zip](https://github.com/Nesvilab/FragPipe/files/7500771/Output_tables.samples.256.257.258.and.Combined.zip)

Hi Felipe@prvst Any luck with the output files? Thanks.

Hi Felipe@prvst Unfortunately the three issues described above in my first two comments have not been sorted out, namely - 1. There are many cases where the number of unique...

To confirm, what are the latest releases? I believe I may have used the version before the latest.

No. I used 4.1 and Fragpipe 17. Do these new versions eliminate all three problems I listed above today?