MassIVE MSV000090952

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GNPS - A comprehensive lipidomic workflow for multi-cohort population phenotyping using stable isotope dilution targeted liquid chromatography-mass spectrometry

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Description

Dysregulated lipid metabolism underpins many chronic diseases including cardiometabolic diseases. Mass spectrometry-based lipidomics is an important tool for understanding mechanisms of lipid dysfunction and is widely applied in epidemiology and clinical studies. With ever-increasing sample numbers, single batch acquisition is often unfeasible, requiring advanced methods that are accurate and robust to batch-to-batch and inter-day analytical variation. Herein, an optimised comprehensive targeted workflow for plasma and serum lipid quantification is presented, combining stable isotope internal standard dilution, automated sample preparation, and ultra-high performance liquid chromatography-tandem mass spectrometry with rapid polarity switching to target 1163 lipid species spanning 20 sub-classes. The resultant method is robust to common sources of analytical variation including blood collection tubes, haemolysis, freeze-thaw cycles, storage stability, analyte extraction technique, inter-instrument variation and batch-to-batch variation with 820 lipids reporting a relative standard deviation of <30% in 1048 replicate quality-control plasma samples acquired across 16 independent batches (total injection count= 6142). However, sample haemolysis of greater than 0.4% impacted lipid concentrations, specifically for phosphatidylethanolamines (PEs). Low inter-instrument variability across two identical LC-MS systems indicated feasibility for intra-/inter-lab parallelisation of the assay. In summary, we have optimised a comprehensive lipidomic protocol to support rigorous analysis for large-scale, multi-batch applications in precision medicine. [doi:10.25345/C5NP1WQ4S] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Lipidomics ; Lipids ; Lipid profiling ; Metabolic phenotyping ; Liquid chromatography-mass spectrometry ; Lipid quantification ; Molecular epidemiology

Contact

Principal Investigators:
(in alphabetical order) 		Monique Ryan, Murdoch University, Australia
Submitting User: monique_ryan
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GNPS content goes here (MSV000090952 [task=615d61adf8fc4a6097be84dc8e34b72b])
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.