The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

Mass Spectrom Rev. 2020 May;39(3):229-244. doi: 10.1002/mas.21540. Epub 2017 Jul 9.


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.

Keywords: informatics; quantitative mass spectrometry; targeted proteomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Animals
  • Humans
  • Mass Spectrometry / methods*
  • Proteins / chemistry*
  • Proteomics / methods*
  • Software


  • Proteins