A comprehensive solution for bottom-up proteomics data analysis

MS-Angel is a free and open-source software tool designed for the analysis of bottom-up proteomics data. It streamlines the configuration and execution of advanced algorithms for peptide identification and quantification. With its intuitive user interface, MS-Angel simplifies workflow creation, execution, inspection, and sharing, making it an ideal choice for researchers and laboratories working with mass spectrometry data. MS-Angel seamlessly integrates with the Proline Web viewer, forming a complete suite for proteomics data analysis, statistics, and visualization.

Key Features

• Modular Workflow Support: MS-Angel supports both classical label-free approaches with DDA or DIA data, and allows for flexible, customizable workflows. Users can select from a range of compatible tools and combine them to create tailored workflows. The system also supports the execution of custom scripts within workflows for maximum flexibility.

• Machine Learning Integration: MS-Angel incorporates machine learning-based MS2 prediction, enhancing identification accuracy and enabling deeper data analysis, especially for complex datasets such as PTMs, proteogenomics, or immunopeptidomics. This feature significantly improves quantification depth without sacrificing accuracy.

• Thermo FAIMS Quantification: MS-Angel provides a simple, checkbox-activated feature to quantify Thermo FAIMS data, which is often more complex than conventional data. This feature simplifies the handling of FAIMS data, a major advantage for users working with such advanced techniques.

• Task Scheduling and Cluster Execution: MS-Angel features an intelligent task scheduler that optimizes the use of computer resources, balancing workloads across tasks and managing parallel execution. Additionally, MS-Angel supports running tasks on server clusters, making it ideal for CPU-intensive operations like MS2Rescore and DIA-NN computations.

• File Watcher for High-Throughput Analysis: MS-Angel includes a file watcher system that enables real-time data processing as raw files become available. This feature allows efficient analysis of high-throughput datasets, improving workflow efficiency and reducing hardware strain.

• Reproducibility and Data Tracking: MS-Angel ensures reproducibility by automatically recording workflow configurations and task logs. It uses MongoDB to store execution records, allowing users to track every step of the process and easily reproduce analyses with consistent settings.

• Proline Web Interface: MS-Angel integrates with Proline Web, a simplified, lightweight interface for quantitative data inspection. While MS-Angel handles workflow configuration, Proline Web enables users to inspect data at the protein, peptide, and precursor levels with an interactive viewer for chromatographic retention alignments and extracted ion chromatograms.

Seamless Integration and Flexibility

MS-Angel’s design follows a client-server architecture, with a backend for task management and execution and a frontend GUI for customizing workflows and managing parameters. It can be deployed as a full bundle or with separate components, ideal for high-performance server deployments and remote workstation access. MS-Angel’s flexible architecture and robust scheduling make it a perfect fit for both individual users and multi-user environments.

Whether you’re working with single-cell proteomics, large-scale proteogenomics, or advanced MS techniques, MS-Angel is a versatile and powerful tool that can adapt to your specific research needs.

Open-Source and Continuously Evolving

As an open-source project (will be soon on github), MS-Angel is constantly evolving and regularly integrates new tools and modules, ensuring that it stays at the forefront of proteomics data analysis.