Hello,

I had an idea for an enhancement request. There is a workaround involving highlighting potentially 100's of lines and deleting them, it just isn't as nice. I created a targeted assay in a two-proteome mixture, and before performing a dilution curve that would take a few days, wanted to confirm with a quick experiment that the peptides chosen were from one proteome and not the other. Two replicates were injected and imported at each of two concentrations, and a Group comparison performed between the concentrations. The sorted Bar plot does a good job to show which peptides do not exhibit the expected fold change. Using Refine / Advanced / Group Comparison and entering a Fold change value appears to be useful in the case where one is interested in peptides that change by more than some ratio, up or down. But in this case, I am interested in accepting peptides with a range of acceptable fold change values, for example between 0.5 and 1.5, and rejecting the others. Does that make sense? Something you could add to your queue of new features?

A related feature request for these types of two-proteome experiments is the ability to filter out peptides that are homologous between organisms. This comes up also when using a carrier proteome: one wants to make sure not to pick peptides that could possibly exist in the carrier proteome. One could imagine a filter tool that allows to enter a path to another fasta file, and to filter out any peptides in common between the current document fasta and that one.

Thanks
Philip