uw-maccosslab / iontrap_vs_orbitrap

Analysis code used in the manuscript "Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring"

This repo contains the basic analyses used in manuscript "Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring"

Folder "bin" contains following scripts:

- make_figures.R: script with functions to make each of the plots in the body of the paper
- calculate_loq.py: script used to calculate and optimize LoQ's, modified from Pino et al (2020)
- load_file_by_header_columns.py: utility script for LOQ analysis
- Optimize_transitions.ipynb: Jupyter notebook containing the commands used to optimize transitions 
- make_figures_supp.R: script with functions so make supplemental figures
- extract_metadata.py: script to extract scan information from mzML files

Folder "data" contains all data files called in the scripts found in bin. All documents come directly from Skyline document grid or are generated by one of the scripts in bin.