On May 4th, 2021, Brendan MacLean presented the topic "Skyline processing of proteome-wide DIA of a controlled mixture" for the second day of the 2021 May Institute hosted by the Vitek lab at Northeastern University.  This webinar session focused on reprocessing the data from Bruderer, MCP 2015. The original published data can be found on PeptideAtlas (Accession PASS00589, the username is PASS00589 and the password is WF6554orn).

This folder on PanoramaWeb is an attempt to capture all of the data and files used in that presentation to make them publicly available in a single well organized form that allows public review and even the ability to work through the steps presented yourself. The slides from the presentations (MacLean and Marsh) are attached to this page along with the instructions for creating the template file used for all subsequent batch processing, detailed instructions on setting up and running batch processing with Skyline Batch.

The template Skyline document produced during the presentation is loaded into the Panorama Targeted MS Runs section below:

• Bruderer.sky - the proteomewide template document containing the set of targets from the sample-specific library (tryptic cleavage peptides, excluding duplicate peptides, and proteins with only 1 peptide)

A local copy of the mass spectrometer data files can be found in the Raw Data tab. The R scripts can be found in the Files tab in a "reports" folder. The necessary annotations and reports to build the template from scratch can be introduced in a Skyline session by downloading and opening MSstats_annotations.sky from the "reports" folder.

→ To reprocess the Bruderer data on your computer:

• Install Skyline and Skyline Batch
• Download  Bruderer.bcfg
• Download install_R_packages.R 
• Follow the instructions in Reprocessing Bruderer Data With Skyline Batch.pdf.