R code repository for the manuscript on Top-Down LC-MS analysis of the 103 subjects from ROS/MAP cohorts

• The raw mass spectrometry data can be downloaded at MassIVE repository by MSV000093728 ID.

• The clinical and pathological metadata is protected by Data Use Agreement (DUA) of Rush Alzheimer's Disease Center (RADC)

• The current repository provides the code for the trasparency of the data analysis.

The indended use:

1. run_processing_pipeline.R takes the results of TopPIC MS/MS search and feature finding, FASTA file and number of additional data files and produces two Bioconductor's MSnSet objects with proteoforms quantified using 1) MS1 intensities and 2) spectral counts.

2. run_to_make_figures_and_tables.R recreates most of the figures (both in the main text and the supplementary) and two supplementary tables with the quantitative data on the proteoforms.