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Title: A Skyline Plugin for Pathway-Centric Data Browsing

Abstract

For targeted proteomics to be broadly adopted in biological laboratories as a routine experimental protocol, wet-bench biologists must be able to approach SRM 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-drive DIA data analysis, again utilizing the pathway view to help narrow down the set of proteins which will be investigated. The plugin is backed by the 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.

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1339822
Report Number(s):
PNNL-SA-117929
Journal ID: ISSN 1044-0305; 453040220
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Society for Mass Spectrometry; Journal Volume: 27; Journal Issue: 11
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Degan, Michael G., Ryadinskiy, Lillian, Fujimoto, Grant M., Wilkins, Christopher S., Lichti, Cheryl F., and Payne, Samuel H. A Skyline Plugin for Pathway-Centric Data Browsing. United States: N. p., 2016. Web. doi: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. United States. doi:10.1007/s13361-016-1448-3.
Degan, Michael G., Ryadinskiy, Lillian, Fujimoto, Grant M., Wilkins, Christopher S., Lichti, Cheryl F., and Payne, Samuel H. 2016. "A Skyline Plugin for Pathway-Centric Data Browsing". United States. doi:10.1007/s13361-016-1448-3.
@article{osti_1339822,
title = {A Skyline Plugin for Pathway-Centric Data Browsing},
author = {Degan, Michael G. and Ryadinskiy, Lillian and Fujimoto, Grant M. and Wilkins, Christopher S. and Lichti, Cheryl F. and Payne, Samuel H.},
abstractNote = {For targeted proteomics to be broadly adopted in biological laboratories as a routine experimental protocol, wet-bench biologists must be able to approach SRM 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-drive DIA data analysis, again utilizing the pathway view to help narrow down the set of proteins which will be investigated. The plugin is backed by the 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.},
doi = {10.1007/s13361-016-1448-3},
journal = {Journal of the American Society for Mass Spectrometry},
number = 11,
volume = 27,
place = {United States},
year = 2016,
month = 8
}
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