Global proteome and Phosphoproteome study in fragpipe

[shilly99]

I am new to fragpipe and want to analyze global and phosphoproteome data for WT and Knock out cell line. I have DDA-LFQ data. I am not sure how to set up the experiment.

• Should I analyze phospho WT and global WT separately and compare it with the Knock out condition. or I should do all of it in one experiment.
• Should I use PTM shepherd or not?

Please help.

Thanks!

[fcyu]

Thanks for your interest in FragPipe.

Should I analyze phospho WT and global WT separately and compare it with the Knock out condition. or I should do all of it in one experiment.

I think you should analyze the phospho and global data separately because they have different content and PTM settings.

Should I use PTM shepherd or not?

For the quantitive differential analysis, no, you don't need to use PTM-Shepherd.

In case you need some tutorial, here is one https://fragpipe.nesvilab.org/docs/tutorial_lfq.html in our webpage, and another one used in the US HUPO 2023 short course https://docs.google.com/document/d/1Y3irUF1cPImOWdjvcQo1wZ5Pdqd4jg8bo_PSDOG173k/edit?usp=sharing

Best,

Fengchao