Welcome to PyParse’s documentation!

Authors: Joseph Mason, Francesco Rianjongdee, Harry Wilders, David Fallon

Description

This script will read Liquid Chromatography Mass Spectrometry (LCMS) data in the Waters OpenLynx™ browser report (.rpt) file format or Shimadzu .daml file format, and assigns peaks to compounds specified in a .csv platemap. This assignment is then used to generate heatmaps and other visualisations to compare and contrast different LCMS runs. It was designed specifically for the analysis of data generated from high-throughput chemistry, and is suitable for reaction optimisations, parallel synthesis, library validation experiments and direct-to-biology.

Example Usage

Standard Analysis for a 96-Well Plate for Water’s data

python PyParse.py example_rpt.rpt example_platemap.csv -o new_output_directory

Standard Analysis for a 96-Well Plate for Shimadzu data

python PyParse.py folder_containing_daml_files example_platemap.csv -o new_output_directory

License

Apache 2.0

Copyright

2023 GlaxoSmithKline Research & Development Limited

Indices and tables

• Index

• Module Index

• Search Page

Contents

Contents:

• Installation and Run
  • Pre-Requisites
  • Preparing a Platemap
  • Specifying a Retention Time in the Platemap
  • Running a PyParse Analysis
  • Commonly Used Optional Parameters
• PyParse Outputs
  • Introduction
  • Heatmap
  • Trellised Pie-Charts
  • Compound Summary Table
  • Hit Validation Graph
• Using the Example Dataset
  • Introduction
  • Expected Output
  • Heatmap
• Automatic Impurity Detection and Reporting
  • Background
  • C-H Activation Reaction Optimisation Plate
  • Conclusions
• Filtering by Retention Time
  • Usage
• Frequently Asked Questions
  • Which UPLC/LCMS Vendors are Supported?
  • Which plot type heatmap should I look at?
  • What does “corrP/STD” actually mean?
  • My plate design has deliberate gaps/empty wells in it - what do I do?
  • I’d like to view the results in Excel/Spotfire/another program - how do I do this?
  • The program didn’t find my product!!
  • The output says “Peak overlap detected!” for my compound – what does this mean?
• Additional Parameters
  • Introduction
  • Generic Parameters
  • Parameters Used for the Analysis
  • Parameters Used for the Visualisations
• PyParse Function Detail
• Acquire Data from Water’s .rpt File
• Acquire Data from Shimadzu .daml Files