Skyline Batch

Skyline Batch automates reprocessing of Skyline documents and associated local or remote mass spectrometry data to enable reproducible proteomics and metabolomics analyses.

Key Features:

• Automated reprocessing: Facilitates automated reprocessing of local and remote files using Skyline without requiring manual command-line execution.
• Configuration-driven workflows: Uses configuration files that encapsulate all processing steps and initiate a predefined four-step workflow within Skyline.
• Remote file retrieval: Downloads necessary files from specified repositories as part of the reprocessing workflow.
• Transparency and reproducibility: Condenses the entire processing workflow into a single configuration file to improve transparency and reproducibility of data processing.

Scientific Applications:

• Proteomics: Automates reprocessing of mass spectrometry data and Skyline documents for proteomics studies.
• Metabolomics: Automates reprocessing of mass spectrometry data and Skyline documents for metabolomics studies.
• Collaborative and large-scale studies: Supports reprocessing of local and remote datasets for laboratory-based and multi-site collaborative projects.

Methodology:

Downloads specified files from repositories and executes a predefined four-step workflow within Skyline as directed by a configuration file.