Hi all,

I am using Proteome Discoverer 2.4 and want to group my replicates (three per condition). From this I want to be able to compare across different conditions based on all three replicates of each condition. E.g: 2 of the 3 replicates of condition A identified Protein A, but 0/3 replicate from condition B identified Protein A.

This way, the data analysis will allow me to compare data across replicates for different conditions (e.g. Condition A vs Condition B) rather than comparing individual replicates (Rep 1 of Condition A vs Rep 1 of Condition B). I want to be able to illustrate (possibly using a Venn Diagram); the number of peptides that condition A identifies, the number of peptides that condition B identifies and the number of peptides that both conditions identify. This could be such that if 2/3 or 3/3 replicates of the condition contain the peptides, then it is deemed to be present in this condition.

I hope this makes sense, and any help will be greatly appreciated. I am currently using PD 2.4

Thanks!