On May 5th, 2021, Brendan MacLean presented the topic "Skyline based comparison of refined vs proteome-wide queries of DIA experiments" for the third day of the 2021 May Institute hosted by the Vitek lab at Northeastern University.  This webinar session focused on reprocessing the data from Selevsek, MCP 2015. The original published data can be found on ProteomeXchange (via the PRIDE partner repository with the data set identifier PXD001010).

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 presentation are attached to this page along with the instructions for creating the template file used for all subsequent batch processing, and 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:

• Selevsek.sky - the unrefined proteomewide template document containing the set of targets from the deep fractionation library (excluding semi-tryptic cleavage peptides, duplicate peptides, and proteins with only 1 peptide)

The original mass spectrometer DIA data files can be found in the Raw Data tab in the "wiff-rep" and "wiff-os" folders.  The R scripts can be found in the Files tab in the "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. And the DDA peptide search results can be found in the folder "dda" in the Raw Data tab.

→ To reprocess the Selevsek data on your computer:

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