Orbitrap notch

A study of the 'notch' in Orbitrap TMT reporter ion intensities.

Now published in ACS Measurement Science Au: https://pubs.acs.org/doi/10.1021/acsmeasuresciau.1c00053

Dependencies:

• R >= 4.0.3
• tidyverse (CRAN)
• ggbeeswarm (CRAN)
• gtools (CRAN)
• MSnbase (Bioconductor)
• limma (Bioconductor)
• biobroom (Bioconductor)
• rawDiag (https://github.com/fgcz/rawDiag)
• camprotR (https://github.com/CambridgeCentreForProteomics/camprotR)

Study components

1. Re-analysis of published datasets to examine:
   • What proportion of PRIDE Orbitrap submissions used Tune < 3.0?
   • Can sub-notch values be removed by average S/N filtering?
   • What happens to notch values?
2. Analysis of a benchmark human:yeast dataset to examine the impact of the notch/sub-notch region on :
   • PSM/peptide/Protein-level fold-change estimates
   • Detection of differentially abundant peptides/proteins

Both analysis subdirectories have the same structure:

• raw: PSM-level inputs
• shared files: Reference and cRAP fasta files
• notebooks: Analyses, with order indicated by prefix
• results: Intermediate and final outputs from notebooks and plots