Duke Proteomics Core - Skyline for Small Molecules

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 Submitter: 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
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DDR2_chromatogram4.sky.zip2021-04-07 18:02:20102811
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LINCS_P100_DIA_Plate23_annotated_minimized_2018-05-02_18-13-55.sky.zip2021-03-19 20:17:48900192960960
LINCS_P100_DIA_Plate24_annotated_minimized_2018-05-02_19-07-44.sky.zip2021-03-19 20:17:489001927329696
LINCS_P100_DIA_Plate27_annotated_minimized_2018-05-02_19-16-47.sky.zip2021-03-19 20:17:489001921,0649696
LINCS_P100_DIA_Plate30_annotated_minimized_2018-05-02_18-33-32.sky.zip2021-03-19 20:17:489001927859696
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LINCS_P100_DIA_Plate34_annotated_minimized_2019-08-30_17-25-21.sky.zip2021-03-19 20:17:489001927529696
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tSIM-PRM_ACO3-Ser91_WT_vs_aco3.sky.zip2021-02-25 10:10:4910310620
T11X_R2021-02-23 07:17:231075640
T11X_QS2021-02-23 07:17:23101814440
T6X_ACDE2021-02-23 07:17:23103628840
T6X_FGHIL2021-02-23 07:17:23103628840
A7X_KMNP2021-02-23 07:17:23103628840
A7X_QS2021-02-23 07:17:23101814440
R8X_ACDEFGH2021-02-23 07:17:23102116840
K9X_ACDE2021-02-23 07:17:23103628840
K9X_KMNP2021-02-23 07:17:23103628840
K9X_QS2021-02-23 07:17:22101814440
A1X_QS2021-02-23 07:17:22101814440
A1X_R2021-02-23 07:17:221075640
A1X_ACDE2021-02-23 07:17:22103628840
T3X_FGHIL2021-02-23 07:17:22103628840

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