lcms_processing.ipynb is an Interactive Python Notebook which takes in an Excel file from the LC-MS (after certification of the calibration points and peak selection) and can be used to obtain blank-subtracted concentrations, limit of quantifications, and quality control data.

lcms_processing_functions.py is a Python Script which performs the actions of formatting the LC-MS Excel file, calculating a calibration curve for each compound, calculating concentrations of samples, subtracting the extraction blank concentration, then calculating replicate statistics and precisions for duplicate, spike, and QC samples.

output_dataframes.py is a Python Script which formats the processed data (including LOQ, concentrations, and precisions) in a way which can be easily visualized at the end of lcms_processing.ipynb

name_replacement.ipynb is an Interactive Python Notebook which can be used to easily reformat sample names to be compatible with the processing script.

LC-MS Procedural Naming Guide.docx is a Word Document which provides instructions for how to designate each type of measurement (calibration, blank, control, sample, duplicate, spike, extraction blank, quality control, and wash) to be compatible with the processing script.

Written by Ethan J. Sontarp and Colin P. Thackray