Atlas is a Nextflow-based pipeline developed for the processing and analysis of mass spectrometry data, specifically designed to assist proteomics laboratories with daily quality assessments across various proteomics applications. It supports multiple workflows, such as regular proteomes, phosphoproteomes, and independent acquisition modes, among others.
With these diverse workflows, Atlas extracts critical quality control parameters, simplifying the evaluation of mass spectrometry experiments. Atlas can be configured to use various search engines, including:
The pipeline is implemented using the latest Nextflow DSL2 syntax and is designed to operate efficiently in HPC (High-Performance Computing) environments.
For more detailed information, please refer to the documentation.
The Atlas pipeline was initially developed by @rolivella.
We would like to express our gratitude to the following individuals for their valuable contributions during the development:
- Eduard Sabidó (@edunivers)
- Cristina Chiva
- Eva Borràs
- Guadalupe Espadas
- Olga Pastor
- Enrique Alonso
- Selena Fernández
A comprehensive list of references for the tools utilized in the pipeline can be found in the CITATIONS.md file.