MacCoss - 2015-Selevsek

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:

  Attached Files  
   
 2021 NEU Day 3 (MacLean).pdf
 Selevsek Data Settings.pdf
 Reprocessing Selevsek Data With Skyline Batch.pdf
 Configuring Skyline Batch for Selevsek Data.pdf

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Selevsek-all.sky.zip2021-11-11 17:50:383,59877,764101,452608,712184 
Selevsek-lowcv.sky.zip2021-11-11 17:10:422,07924,56024,566147,396184Selevsek-all.sky.zip
Selevsek-reps.sky.zip2021-11-11 16:59:013,59877,764101,452608,71284Selevsek-lowcv.sky.zip
Selevsek.sky.zip2021-11-10 19:40:063,59738,88950,764304,58404Selevsek-reps.sky.zip
Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline
Data License: CC BY 4.0 | ProteomeXchange: PXD029665 | doi: https://doi.org/10.6069/2w4t-j381
  • Organism: Saccharomyces cerevisiae
  • Instrument: TripleTOF 5600
  • SpikeIn: No
  • Keywords: Skyline, workflow, reproducible, data analysis, reprocessing, software, mass spectrometry
  • Lab head: Michael MacCoss Submitter: Brendan MacLean
Abstract
Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.
Created on 11/10/21, 8:57 PM