The Skyline Ecosystem: Informatics for Quantitative Mass Spectrometry Proteomics

By Lindsay K. Pino, B. Searle, James G. Bollinger, B. Nunn, Brendan MacLean, Michael J. MacCoss. Mass spectrometry reviews (Print), 2017

676 citations recorded by the source corpus.

Skyline is a freely-available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally-assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/29eb4a91ef11efdbe8161522c7cccbd523e6e1a7

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Citations in the corpus

The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics (2019, methodology): “General functionality/web visualization Dataset centric view Yes Yes Yes Yes Yes Yes Yes Protein centric view across resource Yes Yes (23) Yes Annotated mass spectra Yes Yes Yes Yes Yes Yes Yes Chromatograms Yes Yes Support for RPXD datasets Yes Yes Standalone tools for re-using datasets Data Visual”
High-precision plasma β-amyloid 42/40 predicts current and future brain amyloidosis (2019, methodology): “The precursor/product ion pairs utilized were chosen as previously described(12,19) and the derived integrated peak areas were analyzed using the Skyline software package.(20) For each isotopomer ((14)N or (15)N) of the Aβ isoforms (Aβ38, Aβ40, or Aβ42), integrated peak areas for selected product io”
The ProteomeXchange consortium at 10 years: 2023 update (2022, methodology): “Additionally, there are other open formats produced by the Skyline software (20) that are supported by Panorama Public for ‘Complete’ submissions.”
Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics (2020, background): “10 While small molecule analysis via mass spectrometry has benefitted greatly from technological advances in mass spectrometry and separations science, there remains a need for data analysis with MS vendor-independent software tools that increase transparency and facilitate the translation of…”