Test the results of your method versus global protein copy numbers in your cell.
While the number of proteins and peptides identified in a proteomics experiment is a valuable metric, the distribution of the proteins identified can be a valuable reference point.
This Shiny App is based on the Proteomic Ruler Approach developed by Wizniewski et al., in a simplified form.
Load a CSV of your protein UniProt Accessions and it will plot the distribution of those proteins.
You can download the HeLa Proteomic Ruler result from Bekker-Jennsen et al., here (depth of 14,000 proteins) and two example files to base your results uploads on here and here.
Not interested in HeLa?