Skyline Batch is an application that automates a common Skyline workflow for batch processing Skyline documents. It interacts with Skyline through the command-line, allowing it to import data into a template document, export reports, and run R scripts on those reports without bringing up the Skyline user interface.

Install Skyline Batch for Skyline 20.2 or later, or Skyline-daily (20.2.1 or later)

Skyline Batch Documentation

Skyline Batch Webinar

A hands-on demonstration displaying the depth of Skyline Batch as well as new features:

Webinar 20: Using Skyline Batch for Large-Scale DIA

Skyline Batch Tutorials

Learn how to use Skyline Batch by completing the supplementary tutorials on the Webinar 14 and 15 pages:

Webinar 14: Large Scale DIA with Skyline

Webinar 15: Optimizing Large Scale DIA with Skyline

Skyline Batch Release Notes

Skyline Batch 21.1.0.187 (July 6th, 2021)

• Skyline template files, annotation files, data files, and R scripts can now be downloaded from Panorama
• New download data files dialog that includes an interactive list of the files to be downloaded
• Improved Skyline Batch configuration files that are more easily readable in a text editor
• Updated run button options

Skyline Batch 21.1.0.146 (May 26th, 2021)

• Added a "download files only" run option
• Allow waiting configurations to be unchecked and removed from the current batch run
• Log improvements
• Data download bug fixes

Skyline Batch 20.2.0.475 (Apr. 20th, 2021)

• Can download data files from an FTP server
• Added support for different number formats

Skyline Batch 20.2.0.464 (Apr. 9th, 2021)

• Import configurations by double-clicking a Skyline Batch Configuration file
• No longer requires a Skyline report file for reports that already exist in the template document
• Improved file detection for sharing configurations across computers 

Skyline Batch 20.2.0.453 (Mar. 29th, 2021)

• New option for Skyline file refinement
• Supports using refined files as templates for other configurations
• Added ability to import annotations
• Bug fixes for finding R installations, logging, and more

Skyline Batch 20.2.0.398 (Feb. 2nd, 2021)

• Runs multiple Skyline workflows sequentially
• Displays log of current run
• Allows different configurations to use different Skyline installations
• Supports running R scripts with any version of R