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:
Keywords:
Skyline, workflow, reproducible, data analysis, reprocessing, software, mass spectrometry
Lab head: Michael MacCoss Submitter: Brendan MacLean
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.
Selevsek.bcfg
2021 NEU Day 3 (MacLean).pdf