| Developer(s) | Brendan X. MacLean et al. |
|---|---|
| Initial release | 17 February 2009; 15 years ago (2009-02-17) |
| Stable release | 21.2 |
| Written in | C# |
| Operating system | Windows |
| Type | Bioinformatics / Mass spectrometry software |
| License | Apache license 2.0 |
| Website | Skyline Homepage |
Skyline is an open source software for targeted proteomics and metabolomics 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), parallel reaction monitoring (PRM), data-independent acquisition (DIA/SWATH) and targeted data-dependent acquisition.
See also
References
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.