Fengchao
Fengchao
Hi Matt, > what version did write_uncalibrated_mgf stop working in? Start from the next version. > Or by "used nowhere" did you mean MSFragger users? I am not sure about...
Hi Charlotte, Thanks for the bug reporting. Could you share your mzML and fasta files with me to reproduce the bug? Here is the link to upload the files: https://www.dropbox.com/request/Dqw4R44sptTqttsRXpJK...
Thank you for the files. I have fixed the bug. If you want to try the pre-released version, please send an email to yufe AT umich.edu. Best, Fengchao
Fixed in the latest version. Best, Fengchao
Hi Robert, Thanks for your suggestion. I always want to add such columns as what MaxQuant has, but does not have time to implement it. I will let you know...
Hi Asher, It is calculated by ProteinProphet. If I remember it correctly, it uses all peptides from all samples/input files. Best, Fengchao
That's correct. The protein coverage calculation was not well implemented in Philosopher. We need to change that. Best, Fengchao
The SAINTExpress does not support DIA workflow. We will fix it in the future. Best, Fengchao
It was due to some bugs in @guoci 's Python script. Hopefully, he will have time to revisit them. Best, Fengchao
I just talked to Guo Ci @guoci . He is not willing to resolve this issue. Best, Fengchao