Skyline (software)

Last updated
Skyline
Developer(s) Brendan X. MacLean et al.
Initial release17 February 2009;16 years ago (2009-02-17)
Stable release
21.2
Repository
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 [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.

Contents

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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