A Skyline Plugin for Pathway-Centric Data Browsing

For targeted proteomics to be broadly adopted in biological laboratories as a routine experimental protocol, wet-bench biologists must be able to approach selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) assay design in the same way they approach biological experimental desi...

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Bibliographic Details
Published in:Journal of the American Society for Mass Spectrometry 2016-11, Vol.27 (11), p.1752-1757
Main Authors: Degan, Michael G., Ryadinskiy, Lillian, Fujimoto, Grant M., Wilkins, Christopher S., Lichti, Cheryl F., Payne, Samuel H.
Format: Article
Language:English
Subjects:
Analytical Chemistry
BASIC BIOLOGICAL SCIENCES
Biodiversity
Bioinformatics
Biomonitoring
Biotechnology
Browsing
Chemistry
Chemistry and Materials Science
Data analysis
Focus: Bioinformatics
Laboratories
Mass spectra
Mass spectrometry
MS-Based "Omics": Research Article
Organic Chemistry
Peptides
Proteins
Proteomics
Software
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Description
Summary:For targeted proteomics to be broadly adopted in biological laboratories as a routine experimental protocol, wet-bench biologists must be able to approach selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) assay design in the same way they approach biological experimental design. Most often, biological hypotheses are envisioned in a set of protein interactions, networks, and pathways. We present a plugin for the popular Skyline tool that presents public mass spectrometry data in a pathway-centric view to assist users in browsing available data and determining how to design quantitative experiments. Selected proteins and their underlying mass spectra are imported to Skyline for further assay design (transition selection). The same plugin can be used for hypothesis-driven data-independent acquisition (DIA) data analysis, again utilizing the pathway view to help narrow down the set of proteins that will be investigated. The plugin is backed by the Pacific Northwest National Laboratory (PNNL) Biodiversity Library, a corpus of 3 million peptides from >100 organisms, and the draft human proteome. Users can upload personal data to the plugin to use the pathway navigation prior to importing their own data into Skyline. Graphical Abstract ᅟ
ISSN:1044-0305
1879-1123
DOI:10.1007/s13361-016-1448-3