Detection of small up- or down-regulated Peaks missed by MS/MS

It is well known that in data dependent MS, the MS/MS is focused on the more abundant peptides and therefore will miss many small interesting peaks!

Use the comparative analysis algorithm to find peaks that are different between a sample and control. Then find those peaks for which no MSMS spectrum was acquired. Next perform a new analysis using the MPeaks inclusion list and Identify the real interesting peptides.DiffPeaksLandscape

Increase your coverage at least50%