Succinyl_LOPIT

An extension of LOPIT to explore the subcellular distribution of succinylated peptides

Repository structure:

• raw: PSM-level output from Proteome Discoverer
• shared files: Reference and cRAP fasta files, protein abundances and GO annotations
• notebooks: Analyses in R markdown notebooks, with order indicated by prefix
• results: Intermediate and final outputs from notebooks and plots
• figures: Figure panels for manuscript

Dependencies for notebooks:

• R >= 4.0.3
• tidyverse (CRAN)
• ggrepel (CRAN)
• RColorBrewer (CRAN)
• MSnbase (Bioconductor)
• biomaRt (Bioconductor)
• goseq (Bioconductor)
• pRoloc (Bioconductor)
• camprotR (https://github.com/CambridgeCentreForProteomics/camprotR)
• OptProc (https://github.com/TomSmithCGAT/OptProc)
• pRolocExt (https://github.com/TomSmithCGAT/pRolocExt)