Code and data sets for "Enhancing Peptide-Spectrum Match Identification: Leveraging Mokapot with Nonlinear Machine Learning Algorithms to Increase PSMs, with Consideration for False Positives"

Scripts and Jupyter notebook to recreate figures and rerun the entire pipeline for "Enhancing Peptide-Spectrum Match Identification: Leveraging Mokapot with Nonlinear Machine Learning Algorithms to Increase PSMs, with Consideration for False Positives" manuscript. Please refer to README.md for detailed instruction on the folder structure and how to reproduce the figures.