Along the way, we show that existing methods --- IonQuant, and MaxQuant, and the old version of FlashLFQ --- fail to control the FDR.

The PIP-ECHO method is implemented in the new version of FlashLFQ:

github.com/smith-chem-w...

We make two contributions in this paper: first, a method for ascertaining whether a given technique for peptide identity propagation successfully controls the FDR, and second, a new method, PIP-ECHO, that successfully does this.

When you analyze multiple protein samples in a single MS/MS experiment, it's common to do peptide identity propagation, rescuing peptides that fail to be identified in one run by mapping their coordinates (in time and m/z) from a different run in which those peptides were successfully identified.

Er, let me get back to you on that. 😉