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 (Nov. 2nd, 2021)

  • Remote file sources make downloading files from similar locations easier
  • Added undo/redo functionality for changes to the configuration list
  • Bug fixes for adding R scripts and downloading files from Panorama


Skyline Batch (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 (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 (Apr. 20th, 2021)

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


Skyline Batch (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 (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 (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



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