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Skyline

Free and Open Source Targeted Mass Spec Environment

Description

Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports all types of molecules, with particular support for proteins and peptides. Skyline aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.

Technical Information

Programming languages:
C#, C++, Java, Python
Platforms:
Windows, Wine
Input formats:
Reads Agilent, Bruker, Sciex, Shimadzu, Thermo, Waters, mzXML, mzML, mz5. Imports most search tool outputs.
Output formats:
Iteratively create methods for major mass spec vendors. Custom reports.
Interface:
GUI, CLI, Desktop
Licence:
Apache-2.0 open source

Sections

Section 3 — Targeted Lipidomics (SRM, MRM, PRM)
Section 4 — Lipid Identification (Untargeted)
Section 4.1 — Full MS (HRAM LC-MS)
Section 4.2 — Data Dependent Acquisition (DDA)
Section 4.3 — Data Independent Acquisition (DIA)
Section 4.4 — Ion Mobility Separation
Section 5 — Lipid Quantification (Untargeted)
Section 6 — Analysis and Visualisation
Section 7.1 — Lipid Annotations and ID Converters
Section 7.2 — Lipid Ontology Enrichment Analysis