Comparison of projects before and after manual validation. The Project-comparer tool is useful for comparing a project before and after adjustments are made. The project is initially saved before any adjustment and then saved again under a different name after manual adjustments are made. Two comparative modes are possible. The 'Run-by-Run Analysis' mode shows differences in the deuteration amount calculation between the two projects, reported for each individual experiment ('Run') in the project. The 'Peptide-by-Peptide Analysis' reports differences between the two projects on a per peptide basis.