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.
The CopyNumberPlotter Shiny App is based on the Proteomic Ruler Approach developed by Wizniewski et al., in a simplified form.
Thanks to peer reviewer comments, a second ShinyApp has been developed that allows multiple files to be compared simultaneously. In addition, this new tool generates some useful statistics for the copy number distribution. You can access CopyNumberPlotter V2 here.
For both applications.
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?