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Skyline (software)

{{Infobox software

| name = Skyline

| title =Skyline

| logo =

| logo caption =

| screenshot =

| caption =

| collapsible =

| author =

| developer = Brendan X. MacLean et al.

| released = {{Start date and age|2009|02|17|df=yes}}

| latest release version = 21.2

| discontinued =

| programming language = C#

| operating system = Windows

| platform =

| size =

| language =

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| genre = Bioinformatics / Mass spectrometry software

| license = Apache license 2.0

| alexa =

| website = {{URL|https://skyline.ms/project/home/begin.view?/|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

{{cite journal |vauthors=MacLean B, Tomazela DM, et al. |title=Skyline: an open source document editor for creating and analyzing targeted proteomics experiments |journal=Bioinformatics |volume=26 |issue=7 |pages=966–8 |year=2010 |pmid=20147306 |pmc=2844992 |doi=10.1093/bioinformatics/btq054 }}

{{cite journal |vauthors=Pino L, et al. |title=The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics |journal=Mass Spectrometry Reviews |volume=39 |issue=3 |pages=229–244 |year=2017 |pmid=28691345 |pmc=5799042 |doi=10.1002/mas.21540 }}

{{cite journal |vauthors=Adams K, et al. |title=Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics |journal=Journal of Proteome Research |volume=19 |issue=4 |pages=1447–1458 |year=2020 |pmid=31984744 |pmc=7127945 |doi=10.1021/acs.jproteome.9b00640 }}

{{cite journal |vauthors=Abbatiello S, et al. |title=Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma |journal=Mol Cell Proteomics |volume=14 |issue=9 |pages=2357–74 |year=2015 |pmid=25693799 |pmc=4563721 |doi=10.1074/mcp.M114.047050 |doi-access=free }}

{{cite journal |vauthors=Sherrod S, et al. |title=Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides |journal=Journal of Proteome Research |volume=11 |issue=6 |pages=3467–79 |year=2012 |pmid=22559222 |pmc=3368409 |doi=10.1021/pr201240a }}

{{cite journal |vauthors=Schilling B, et al. |title=Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows |journal=Analytical Chemistry |volume=87 |issue=20 |pages=10222–9 |year=2015 |pmid=26398777 |pmc=5677521 |doi=10.1021/acs.analchem.5b02983 }}

{{cite journal |vauthors=Navarro P, et al. |title=A multicenter study benchmarks software tools for label-free proteome quantification |journal=Nature Biotechnology |volume=34 |issue=11 |pages=1130–1136 |year=2016 |pmid=27701404 |pmc=5120688 |doi=10.1038/nbt.3685 }}

{{cite journal |vauthors=Schilling B, et al. |title=Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation |journal=Mol Cell Proteomics |volume=11 |issue=5 |pages=202–214 |year=2012 |pmid=22454539 |pmc=3418851 |doi=10.1074/mcp.M112.017707 |doi-access=free }}

External links

  • {{URL|https://skyline.ms/project/home/begin.view?/|Skyline Homepage}}

Category:Free science software

Category:Bioinformatics software

Category:Mass spectrometry software

Category:Proteomics

Category:Software using the Apache license