RAW XIC Export

This repository contains a Python script to extract Extracted Ion Chromatograms (XICs) from Thermo Fisher Scientific RAW mass spectrometry files. The script leverages the ThermoRawFileParser to access and convert RAW data for subsequent XIC extraction based on specified m/z values.

Features

• XIC Extraction: Extracts chromatographic data for specified m/z values with a user-defined tolerance.
• Docker Compatibility: Runs with Docker for cross-platform use, or locally on compatible systems.
• User-Defined Ions: Specify a list of m/z values for targeted ion extraction.
• Output Options: Generates outputs for downstream analysis.

Requirements

• Python 3.x
• Docker
• pandas
• pyrawr

Installation

1. Clone the Repository:

   git clone https://github.com/wilhan-nunes/raw-xic-export.git
   cd raw-xic-export

2. Install Dependencies:

   pip install pandas pyrawr

3. ThermoRawFileParser:

   Download and install ThermoRawFileParser or use the Docker version specified in the script.

Usage

1. Specify Ions and Tolerance:

   In raw_parser.py, specify the ions of interest in ion_list with m/z values and tolerance settings.

   ion_list = ['164.107', '178.1226', '192.0689', '192.1383', '206.1539']

2. Execute the Script:

   Run the script to extract ions from RAW files in the specified directory.

   python raw_parser.py

3. Docker Execution:

   Ensure Docker is installed and running. Adjust Docker image paths in the script if needed. If running on windows/linux, please refer to the pyrawr documentation for more details.