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Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Open accessAbstract
Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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“For example, the targeted MS quantification method based on selected reaction monitoring [132–134] was recently implemented to understanding the transmission of a plant virus.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [132]
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Cites
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Metadata
- Authors
- MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., & MacCoss, M. J.
- Affiliations
- Microsoft (United States) (US)
- Corresponding author
- MacLean, Brendan
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-02-09
- Volume
- 26
- Issue
- 7
- Pages
- 966-968
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2844992
- OpenAlex
- W2141091417
- Cited by
- 4,697
- References
- 9
- Citations by year
- 2026: 248 · 2025: 308 · 2024: 400 · 2023: 391 · 2022: 386 · 2021: 436 · 2020: 465 · 2019: 390 · 2018: 324 · 2017: 326 · 2016: 301 · 2015: 236 · 2014: 192 · 2013: 131 · 2012: 94
- FWCI
- 42.28
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute on Aging (P30AG013280)
- National Heart, Lung, and Blood Institute (R01HL082747)
- National Cancer Institute (U24CA126479)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK069386)
- National Center for Research Resources (P41RR011823)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- skyline, targeted proteomics, multiple reaction monitoring, open source software, dynamic report generation
- MeSH terms
- Software, Mass Spectrometry, User-Computer Interface, Databases, Protein, Proteomics
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