The msDiaLogue Cookbook

Welcome

Welcome to the msDiaLogue Cookbook!

This book provides practical, example-driven recipes for analyzing mass spectrometry-based proteomics data using msDiaLogue in R. Each recipe focuses on one module of the analysis workflow, allowing users to easily combine recipes into workflows that best fit their own analyses.

What is msDiaLogue?

msDiaLogue is an R package developed through a collaboration between the Proteomics & Metabolomics Facility (PMF) and the Statistical Consulting Services (SCS) at the University of Connecticut (UConn) It provides a modular workflow for analyzing untargeted mass spectrometry (MS)-based proteomics data, together with a wide range of visualization options for both Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) datasets.

UConn CORE SCS

Design philosophy

Unlike monolithic analysis pipelines, msDiaLogue is designed as a modular workflow. Each analysis step is implemented as an independent module that can be used on its own or combined with other modules. This design allows users to adapt the workflow to different experimental designs, software platforms, and analysis objectives.

Workflow

Organization of this cookbook

The cookbook is organized into independent recipes corresponding to the major modules of msDiaLogue. Each chapter introduces one module using practical examples and can be read independently. Readers may follow the recipes in sequence as a complete workflow or use individual chapters as references for specific analysis tasks.