This repository contains teaching material for the 3rd International Summer School on Non-Targeted Metabolomics Data Mining for Biomedical Research.
Non-invasive drug monitoring is desirable as it improves patient experience. Instead of relying on invasive blood draws drug pharmacokinetics and metabolism could for example be monitored through the skin. During the summer school, you will be working with a subset of the data published by Panitchpakdi and collaborators (2022). The datasets consists of plasma and skin swabs (forearm, forehead and upper back) collected from healthy volunteers (n=7) over the course of 24 hours, who have been administered the antihistaminic diphenhydramine. Your task will be to investigate whether:
- Diphenhydramine and its metabolites can be detected in the skin and whether it exhibits similar pharmacokinetics as in plasma?
- You can observe other metabolites that exhibit interesting time trends in plasma and whether those metabolites can also be detected in the skin?
Metabolomics mass spectrometry data are publicly available in the open .mzML/.mzXML format at: MSV000092389
As a student you will be divided into two groups. Group 1 will be working with skin samples collected from the forehead, whereas Group 2 will work on skin samples collected from the forearm. Both groups will be investigating whether their respective skin samples could be suitable for non-invasive drug monitoring by comparing them to the plasma samples. The instructor team will be be working with skin samples collected from the upper back.
Preprocessed data are available in the subfolders data/mzmine_output. [We added some placeholders for now, MZmine 3 team, please replace with the corresponding outputs for downstream analysis]
Mass spectral molecular networks of the data are publicly accessible through the links below.
[GNPS team, please add links below after MZmine 3 team uploads data outputs]
Example: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6c9c4b22970f448d933a6fc7fa13227e
Group 1: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a2baed56d46648898aad480f9e484160
Group 2: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=ca64bf41771b4152a3f94cc09b93c546
Example jupyter notebooks used for data analysis are available in the subfolder notebooks.
Interactive jupyter notebooks can be launched in Google Colaboratory here:
