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. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. J Proteome Res [Internet]. 2020 Jan 27; Available from: https://doi.org/10.1021/acs.jproteome.9b00640
Skyline, Small Molecules, Metabolomics, Pharmacokinetics, Quantification, Mass Spectrometry, Selected Reaction Monitoring, Targeted Mass Spectrometry, High-Resolution, Untargeted Mass Spectrometry
Lab head: Will Thompson Submitter: Will Thompson
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 quantitative mass spectrometry method development and data processing with a ten-year history supporting 6 major instrument vendors. Designed initially for proteomic analysis, we describe the expansion of Skyline to data for small molecule analysis, including selected reaction monitoring (SRM), high-resolution mass spectrometry (HRMS), 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.
Various experiments to demonstrate the performance of Skyline for small molecule quantification, including SRM analyses, SRM method development, positive/negative switching SRM, and high-resolution MS1 quantification.