Default parameters in MS2 Rescore

[TheB1307]

Dear community

I am using MS2 Rescore for processing my data which were identified with Sage. There I used 100 % FDR. Now, I run MS2 Rescore and I am wondering how high the FDR is. I tried to find a solution in the output files and in the paper which were published. But I can't find an answer. Also if I am able to change the number or it is by default always 1 %? Can somebody help me with that?

Have a great day!

[RalfG]

Hi @TheB1307,

Thanks for the question! MS²Rescore always returns all PSMs without FDR filtering (so 100%). The ms2rescore.psms.tsv file has a q-value column that can be used to filter the PSMs. For instance, only keeping rows with q-value < 0.01 will result in a file that is filtered on 1% FDR. Note that decoy PSMs are also included.

The same is true for the mokapot.psms.txt, mokapot.peptides.txt and mokapot.proteins.txt files, although these only contain target PSMs with decoy PSMs having their own respective text files.

We can easily add a configuration parameter to write only target PSMs filtered at an FDR threshold. I will open an issue for this.

Best,
Ralf

[TheB1307]

Hi @RalfG

Thank you so much for your answer! That's really helpful. And thank you for adding the additional parameter :) I am using the function to write a FlashLQF-file so I directly can use it for the next step. Would be great to directly use the file instead of an additional filtering step.

Have a great day!
Best wishes!

[RalfG]

Hi @TheB1307,

Do you use MS²Rescore's built-in output for FlashLFQ? This enables Mokapot's to_flashlfq function, which by default only contains confident target peptides. So no further filtering is required on this output file.

Best,
Ralf

[TheB1307]

Hi @RalfG
Yes, I use this! That sounds great! thank you so much for the answer.
Best!