Machine Learning-based Filtering of Nt-arginylome and Corresponding PRM Algorithm for Validation.

End-to-end pipeline for high-confidence identification and validation of N-terminal arginylation (Nt-Arg) from N-terminomics data. The workflow implements a two-stage search, MS2/RT transfer-learning–based rescoring, and optional PRM validation with paired peptides (Nt-Arg vs unmodified). The repo includes RMarkdown notebooks that reproduce the main analyses and figures from the manuscript. For N-terminome Part: NterminomeAnalysis.Rmd :: outlined codes in Rmarkdown format with detailed explanation for data reading to data tranformation for ML-based filtering. figures_nterminome.Rmd :: outlined codes in Rmarkdown format with detailed explanation for figure generation in the paper (not yet published). .Rdata:: Rdata file containing all objects to test-run codes. project file: a Rstudio project file. For PRM Part: PRM_INCLUSIONLIST.Rmd :: outlined codes in Rmarkdown format with detailed explanation for algorithm to acquire inclusion list for the targets using ML-based prediction. PRM_RESULT_TRNASLATION.Rmd :: outlined codes in Rmarkdown format with detailed explanation for algorithm to translate the PRM raw file using the inclusion list. This code includes theoretical and predicted spectra generation and matching. PRM_figures.Rmd :: outlined codes in Rmarkdown format with detailed explanation for figure generation in the paper (not yet published).