MassIVE MSV000084849

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GNPS - Supplemental Data For: Lipid Annotator: Towards Accurate Annotation in Non-Targeted LC-HRMS/MS Lipidomics Using A Rapid and User-Friendly Software

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Description

This data was used in the manuscript: "Lipid Annotator: Towards Accurate Annotation in Non-Targeted LC-HRMS/MS Lipidomics Using A Rapid and User-Friendly Software" Aliquots (40 uL for (+ mode) and 120 uL for (- mode)) of thawed plasma (NIST SRM 1950 Metabolites in Frozen Plasma, Sigma, St. Louis USA) were each extracted using a modified Folch extraction procedure and reconstituted in 100 uL of a methanol/chloroform mixture (9:1, v/v). LC separation was performed on an Agilent 1290 Infinity II LC System, with a 19 min gradient time on a reverse phase C18 column (Agilent InfinityLab Poroshell 120 EC-C18, 3.0 x 100 mm, 2.7 um). Mobile phase consisted of 10 mM ammonium acetate and 0.2 mM ammonium fluoride in 9:1 water/methanol, while mobile phase B consisted of 10 mM ammonium acetate and 0.2 mM ammonium fluoride in 2:3:5 acetonitrile/methanol/isopropanol. Negative and positive polarity data was acquired on the Agilent 6546 LC/Q-TOF using iterative MS/MS acquisition mode on 6 injections of extracted plasma for each polarity. Detailed experimental methods for chromatography and mass spectrometry can be found in in the Agilent application note 5994-0775en. Two methods were used, a high-load and a low-load method, to determine the effect of high injection volumes / concentration on the number of annotations using the Agilent 6546 LC/Q-TOF. [doi:10.25345/C5NT2F] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: lipidomics ; lipid annotation ; tandem mass spectrometry ; liquid chromatography ; metabolomics ; ion mobility ; automation ; software ; time-of-flight ; Lipid Annotator ; LipidMatch ; MS-DIAL

Contact

Principal Investigators:
(in alphabetical order) 		Jeremy P Koelmel, Yale University, United States
Submitting User: jeremykoelmel
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GNPS content goes here (MSV000084849 [task=a18ac48abb6b4148a41a1ec31e86abb3])
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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.