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Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.

Publication ,  Journal Article
Adams, KJ; Pratt, B; Bose, N; Dubois, LG; St John-Williams, L; Perrott, KM; Ky, K; Kapahi, P; Sharma, V; MacCoss, MJ; Moseley, MA; Colton, CA ...
Published in: Journal of proteome research
April 2020

Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method development and data processing with a 10 year history supporting six major instrument vendors. Designed initially for proteomics analysis, we describe the expansion of Skyline to data for small molecule analysis, including selected reaction monitoring, high-resolution mass spectrometry, and calibrated quantification. This fundamental expansion of Skyline from a peptide-sequence-centric tool to a molecule-centric tool makes it agnostic to the source of the molecule while retaining Skyline features critical for workflows in both peptide and more general biomolecular research. The data visualization and interrogation features already available in Skyline, such as peak picking, chromatographic alignment, and transition selection, have been adapted to support small molecule data, including metabolomics. Herein, we explain the conceptual workflow for small molecule analysis using Skyline, demonstrate Skyline performance benchmarked against a comparable instrument vendor software tool, and present additional real-world applications. Further, we include step-by-step instructions on using Skyline for small molecule quantitative method development and data analysis on data acquired with a variety of mass spectrometers from multiple instrument vendors.

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Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

April 2020

Volume

19

Issue

4

Start / End Page

1447 / 1458

Related Subject Headings

  • Software
  • Proteomics
  • Metabolomics
  • Mass Spectrometry
  • Biochemistry & Molecular Biology
  • Amino Acid Sequence
  • 34 Chemical sciences
  • 31 Biological sciences
  • 06 Biological Sciences
  • 03 Chemical Sciences
 

Citation

APA
Chicago
ICMJE
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Adams, K. J., Pratt, B., Bose, N., Dubois, L. G., St John-Williams, L., Perrott, K. M., … Alzheimer’s Disease Metabolomics Consortium. (2020). Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. Journal of Proteome Research, 19(4), 1447–1458. https://doi.org/10.1021/acs.jproteome.9b00640
Adams, Kendra J., Brian Pratt, Neelanjan Bose, Laura G. Dubois, Lisa St John-Williams, Kevin M. Perrott, Karina Ky, et al. “Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.Journal of Proteome Research 19, no. 4 (April 2020): 1447–58. https://doi.org/10.1021/acs.jproteome.9b00640.
Adams KJ, Pratt B, Bose N, Dubois LG, St John-Williams L, Perrott KM, et al. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. Journal of proteome research. 2020 Apr;19(4):1447–58.
Adams, Kendra J., et al. “Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.Journal of Proteome Research, vol. 19, no. 4, Apr. 2020, pp. 1447–58. Epmc, doi:10.1021/acs.jproteome.9b00640.
Adams KJ, Pratt B, Bose N, Dubois LG, St John-Williams L, Perrott KM, Ky K, Kapahi P, Sharma V, MacCoss MJ, Moseley MA, Colton CA, MacLean BX, Schilling B, Thompson JW, Alzheimer’s Disease Metabolomics Consortium. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. Journal of proteome research. 2020 Apr;19(4):1447–1458.
Journal cover image

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

April 2020

Volume

19

Issue

4

Start / End Page

1447 / 1458

Related Subject Headings

  • Software
  • Proteomics
  • Metabolomics
  • Mass Spectrometry
  • Biochemistry & Molecular Biology
  • Amino Acid Sequence
  • 34 Chemical sciences
  • 31 Biological sciences
  • 06 Biological Sciences
  • 03 Chemical Sciences