A Skyline Plugin for Pathway-Centric Data Browsing

Michael G. Degan, Lillian Ryadinskiy, Grant M. Fujimoto, Christopher S. Wilkins, Cheryl F. Lichti, Samuel H. Payne

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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. [Figure not available: see fulltext.]

Original languageEnglish (US)
Pages (from-to)1752-1757
Number of pages6
JournalJournal of the American Society for Mass Spectrometry
Volume27
Issue number11
DOIs
StatePublished - Nov 1 2016

Fingerprint

Northwestern United States
Protein Interaction Maps
Assays
Biodiversity
Proteome
Proteomics
Libraries
Mass Spectrometry
Data privacy
Proteins
Research Design
Monitoring
Design of experiments
Peptides
Mass spectrometry
Navigation
Experiments

Keywords

  • Bioinformatics
  • Data analysis
  • Systems biology
  • Targeted proteomics

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy

Cite this

Degan, M. G., Ryadinskiy, L., Fujimoto, G. M., Wilkins, C. S., Lichti, C. F., & Payne, S. H. (2016). A Skyline Plugin for Pathway-Centric Data Browsing. Journal of the American Society for Mass Spectrometry, 27(11), 1752-1757. https://doi.org/10.1007/s13361-016-1448-3

A Skyline Plugin for Pathway-Centric Data Browsing. / Degan, Michael G.; Ryadinskiy, Lillian; Fujimoto, Grant M.; Wilkins, Christopher S.; Lichti, Cheryl F.; Payne, Samuel H.

In: Journal of the American Society for Mass Spectrometry, Vol. 27, No. 11, 01.11.2016, p. 1752-1757.

Research output: Contribution to journalArticle

Degan, MG, Ryadinskiy, L, Fujimoto, GM, Wilkins, CS, Lichti, CF & Payne, SH 2016, 'A Skyline Plugin for Pathway-Centric Data Browsing', Journal of the American Society for Mass Spectrometry, vol. 27, no. 11, pp. 1752-1757. https://doi.org/10.1007/s13361-016-1448-3
Degan MG, Ryadinskiy L, Fujimoto GM, Wilkins CS, Lichti CF, Payne SH. A Skyline Plugin for Pathway-Centric Data Browsing. Journal of the American Society for Mass Spectrometry. 2016 Nov 1;27(11):1752-1757. https://doi.org/10.1007/s13361-016-1448-3
Degan, Michael G. ; Ryadinskiy, Lillian ; Fujimoto, Grant M. ; Wilkins, Christopher S. ; Lichti, Cheryl F. ; Payne, Samuel H. / A Skyline Plugin for Pathway-Centric Data Browsing. In: Journal of the American Society for Mass Spectrometry. 2016 ; Vol. 27, No. 11. pp. 1752-1757.
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