Duke Proteomics Core - Skyline for Small Molecules

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

  • Organism: Homo sapiens, Mus musculus
  • Instrument: Xevo TQ-S,Triple Quad 5500,Synapt G2 HDMS
  • SpikeIn: Yes
  • Keywords: Skyline, Small Molecules, Metabolomics, Pharmacokinetics, Quantification, Mass Spectrometry, Selected Reaction Monitoring, Targeted Mass Spectrometry, High-Resolution, Untargeted Mass Spectrometry
  • Lab head: Will Thompson
Abstract
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.
Experiment Description
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.
Sample Description
Brain tissue, urine, plasma, cell culture lysates
Created on 8/22/19, 9:58 PM
Clustergrammer Heatmap
Flag FileDownloadCreatedListsSmall MoleculesPrecursorsTransitionsReplicatesCalibration Curves
Polyamines_Brain_2019-08-22_11-32-25.sky.zip2019-08-22 21:57:4711520609415
Polyamines_1_X_2019-08-22_11-44-35.sky.zip2019-08-22 21:57:4711014435510
DAG_Verification_2019-08-22_11-31-48.sky.zip2019-08-22 21:57:471248132
Biocrates_p180Quantification_UPLC_KJA_Manual_v3_1_x_052819_2019-08-22_11-30-44.sky.zip2019-08-22 21:57:4724271719842
2018-01-18-Iso1-MouseUrine_scan - FINAL_2019-08-22_11-28-52.sky.zip2019-08-22 21:57:4711606811260
Polyamines_Urine_1_X2_2019-08-22_12-08-36.sky.zip2019-08-22 21:57:47161031556

This data is available under the CC BY 4.0 license.