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
- 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)
- 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?
- 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