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Skyline

Topic: Software

 From HandWiki - Reading time: 2 min
Skyline
Developer(s)Brendan X. MacLean et al.
Initial release17 February 2009; 16 years ago (2009-02-17)
Stable release
21.2
Written inC#
Operating systemWindows
TypeBioinformatics / Mass spectrometry software
LicenseApache license 2.0
WebsiteSkyline Homepage

Skyline is an open source software for targeted proteomics[1][2] and metabolomics[3] data analysis. It runs on Microsoft Windows and supports the raw data formats from multiple mass spectrometric vendors. It contains a graphical user interface to display chromatographic data for individual peptide or small molecule analytes.

Skyline supports multiple workflows including selected reaction monitoring (SRM) / multiple reaction monitoring (MRM),[4] parallel reaction monitoring (PRM),[5][6] data-independent acquisition (DIA/SWATH)[7] and targeted data-dependent acquisition.[8]

See also

References

  1. ↑ "Skyline: an open source document editor for creating and analyzing targeted proteomics experiments". Bioinformatics 26 (7): 966–8. 2010. doi:10.1093/bioinformatics/btq054. PMID 20147306. 
  2. ↑ "The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics". Mass Spectrometry Reviews 39 (3): 229-244. 2017. doi:10.1002/mas.21540. PMID 28691345. 
  3. ↑ "Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics". Journal of Proteome Research 19 (4): 1447–1458. 2020. doi:10.1021/acs.jproteome.9b00640. PMID 31984744. 
  4. ↑ "Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma". Mol Cell Proteomics 14 (9): 2357-74. 2015. doi:10.1074/mcp.M114.047050. PMID 25693799. 
  5. ↑ "Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides". Journal of Proteome Research 11 (6): 3467-79. 2012. doi:10.1021/pr201240a. PMID 22559222. 
  6. ↑ "Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows". Analytical Chemistry 87 (20): 10222-9. 2015. doi:10.1021/acs.analchem.5b02983. PMID 26398777. 
  7. ↑ "A multicenter study benchmarks software tools for label-free proteome quantification". Nature Biotechnology 34 (11): 1130-1136. 2016. doi:10.1038/nbt.3685. PMID 27701404. 
  8. ↑ "Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation". Mol Cell Proteomics 11 (5): 202–214. 2012. doi:10.1074/mcp.M112.017707. PMID 22454539. 




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