Skyline (software)

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
Developer(s)Brendan X. MacLean et al.
Initial release17 February 2009 (2009-02-17)
Stable release
21.2
Written inC#
Operating systemWindows
TypeBioinformatics / Mass spectrometry software
LicenseApache license 2.0
WebsiteSkyline Homepage

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. MacLean B, Tomazela DM, et al. (2010). "Skyline: an open source document editor for creating and analyzing targeted proteomics experiments". Bioinformatics. 26 (7): 966–8. doi:10.1093/bioinformatics/btq054. PMC 2844992. PMID 20147306.
  2. Pino L, et al. (2017). "The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics". Mass Spectrometry Reviews. 39 (3): 229–244. doi:10.1002/mas.21540. PMC 5799042. PMID 28691345.
  3. Adams K, et al. (2020). "Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics". Journal of Proteome Research. 19 (4): 1447–1458. doi:10.1021/acs.jproteome.9b00640. PMC 7127945. PMID 31984744.
  4. Abbatiello S, et al. (2015). "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. doi:10.1074/mcp.M114.047050. PMC 4563721. PMID 25693799.
  5. Sherrod S, et al. (2012). "Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides". Journal of Proteome Research. 11 (6): 3467–79. doi:10.1021/pr201240a. PMC 3368409. PMID 22559222.
  6. Schilling B, et al. (2015). "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. doi:10.1021/acs.analchem.5b02983. PMC 5677521. PMID 26398777.
  7. Navarro P, et al. (2016). "A multicenter study benchmarks software tools for label-free proteome quantification". Nature Biotechnology. 34 (11): 1130–1136. doi:10.1038/nbt.3685. PMC 5120688. PMID 27701404.
  8. Schilling B, et al. (2012). "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. doi:10.1074/mcp.M112.017707. PMC 3418851. PMID 22454539.
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