Class FDR, q-values

[ypriverol]

We need to have a way of computing the FDR for classes of PSMs - Peptides and Proteins. This classes can be :

• [ ] General Modified: FDR for peptides modified.
• [ ] Specific Modification FDR. FDR for Phosphorylated Peptides.
• [ ] Misscleavage (0 , 1, 2)
• [ ] CvParam Classification. We can assign to each psm (using cvParam) the tissue, cell type, or disease where it has been found and we can compute the FDR for the specific Characteristic (apart of the global FDR).

In principle, we should be able to get the list of peptides at 1% FDR and remove all the peptides with 2 miscleavages at 0.001% (Misscleavage FDR).

This is really relevant to perform studies like this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974352/