Targeted LC-MS/MS Quality Control and Data Integration Pipeline for PFAS Analysis

The workflow processes high-resolution LC-MS/MS data generated on a SCIEX QTOF instrument and evaluates quality control metrics following EPA 1633A guidelines.

Workflow Overview

Prepare your project folder

Collect all raw input files (exported text files from SCIEX Analyst) into a dedicated project directory. Ensure that this project directory is located in the same parent folder as the scripts (data_analysis.ipynb, create_project_folder.ipynb, and utils.py).

Make sure your instrumentation detection limits are available.

IDL values for various methods are deposited in the lab_parameters directory. If using a new method, calculate instrument detection limits (IDLs) with: calculate_idl.py.

Generate template parameter files

Open create_project_folder.ipynb and set your project_folder variable, so that it points to the project directory containing your raw data. This notebook detects sample and compound names in your raw data and creates input parameter templates:

• eis_paramters.csv
• compound_parameters.csv
• sample_parameters.csv
• simulation_parameters.csv
• mdl_parameters.csv

Once the script run successfully you will find the input files in your project folder under simulation_parameters. Update these files according to your study. Detailed instructions are included in the notebook.

Run the main analysis

Execute data_analysis.ipynb, ensuring the project_folder variable is set correctly.
The notebook will generate:

• an Excel QA/QC report
• a long-format .csv table
  Both will be accessible in your project folder under processed_data.

Dependencies & Folder Structure

Both notebooks create_project_folder.ipynb and data_analysis.ipynb rely on:

• utils.py
• lab_parameters/ Ensure these are stored together if downloaded manually.

Input Data & Naming Conventions

Input files must come from SCIEX Analyst exported tables or Waters Connect. These are either .csv or .txt files.

Files must end with:

• _core → data from the core method
• _extended → data from the extended method

Files to be combined from the same batch must share the same prefix: Example:

• batch_1_core.txt
• batch_1_extended.txt

A complete test set is available in the test/ directory.

Software Requirements

You may run the pipeline in:

• JupyterLab (via Anaconda)
• Google Colab
• Any environment supporting Jupyter notebooks

Definitions

Term	Description
Extracted Internal Standards (EIS)	Mass-labeled standards added before extraction (formerly IDA).
Non-Extracted Internal Standards (NIS)	Standards added after extraction, before injection (also IPS).
Target analytes	PFAS native compounds quantified by LC-MS/MS.
HRMS channel	High-resolution TOF channel used to confirm native ions. For triple quad (mass spec) it is the confirmation channel.
MS/MS channel	Fragmentation channel used for quantification. Also known as quantitation channel.

Video Tutorials

Title	Link
Overview	Youtube Link
What is Code?	Youtube link
QA/QC Briefing	Youtube Link
Step by step instruction (for Sciex data)	Youtube Link
Processing Waters data	Youtube Link

Contact

johanna.ganglbauer@uri.edu

Ackknowledgement

This work is supported by the National Institute of Environmental Health under grant P42ES027706 in superfund research project Sources, Transport, Exposure & Effects of PFAS (STEEP).