Every MS experiment will need some idea of the peptide hit counts that represent noise or unusual features, such as over-represented peptides in the proteome. In this recipe, we'll use some neat visualization tricks using tidyverse tools such as dplyr and ggplot to create graphics that will help you get an idea of the spread and limits of the peptide hits in your mass spectrometry experiment.
Visualizing distributions of peptide hit counts to find thresholds
Getting ready
For this recipe, you'll require the MSnId, data.table, dplyr, and ggplot packages. We'll use the mzid file, HeLa_180123_m43_r2_CAM.mzid.gz, from the datasets/ch6 folder of this book's repository.
