Summary of Study ST002911

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001811. The data can be accessed directly via it's Project DOI: 10.21228/M8MQ7C This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST002911
Study Title	LiLA: Lipid Lung-based ATLAS built Through a Comprehensive Workflow Designed for an Accurate Lipid Annotation
Study Summary	Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However, annotating the wide variety of lipid species in biological samples remains challenging in untargeted lipidomic studies. In this work, we present an optimized lipid annotation workflow based on the combination of LC-MS and MS/MS strategies, four bioinformatic tools, and a decision-tree-based approach to support the accurate annotation and semi-quantification of the lipid species present in lung tissue from control mice. The developed workflow allowed us to generate a lipid lung-based ATLAS (LiLA), which was then employed to unveil the lipidomic signatures of the Mycobacterium tuberculosis (Mtb) infection at two different time points for a deeper understanding of the disease progression. This workflow, combined with manual inspection strategies of MS/MS data, can enhance the annotation process for lipidomic studies and guide the generation of sample-specific lipidome maps. LiLA serves as a freely available data resource that can be employed in future studies to address lipidomic alterations in mice lung tissue.
Institute	Universidad CEU San Pablo
Department	Centro de MEtabolómica y Bioanálisis (CEMBIO)
Last Name	González
First Name	Carolina
Address	km 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501
Email	carolina.gonzalezriano@ceu.es
Phone	646251045
Submit Date	2023-10-02
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2023-10-20
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP003030
Sampleprep Summary:	The sample preparation and lipid extraction were performed at the Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham (Birmingham, AL, United States), following a protocol initially described and optimized at CEMBIO (Madrid, Spain). Approximately 75 mg of lung tissue was mixed with a cold (–20°C) mixture of MeOH:H2O (1:1, v/v) added in a ratio of 1 mg tissue:10 µL of extraction solvent. Next, the tissue samples were homogenized using the Dounce homogenizer. After the homogenization, 200 µL of homogenate was mixed with 640 µL of MeOH and 160 µL of Methyl-Tert-Butyl ether (MTBE) to extract hydrophobic compounds. Samples were then vortex-mixed for 1 hour at room temperature (RT) and centrifuged at 4000 g for 20 min at 20°C. The samples were then passed through spin X columns (0.22 µm filter), and 200 µL of the filtered sample was dried at RT in the vacuum concentrator. From here, the samples were sent to CEMBIO for the UHPLC-MS analysis. Prior to the analysis, dried samples were re-suspended with 200 µL of MeOH/MTBE/H2O (7.4:1.6:1, v/v/v), which contained the corresponding ISs (C17 – sphingosine at 1 ppm for positive ion mode, and d31–palmitic acid at 3 ppm for negative ion mode). Samples were then centrifuged (16,100xg, 5 min, 15°C) before transferring them into sample vials with glass inserts for LC-MS analysis.

Sampleprep ID:

SP003030

Sampleprep Summary:

The sample preparation and lipid extraction were performed at the Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham (Birmingham, AL, United States), following a protocol initially described and optimized at CEMBIO (Madrid, Spain). Approximately 75 mg of lung tissue was mixed with a cold (–20°C) mixture of MeOH:H2O (1:1, v/v) added in a ratio of 1 mg tissue:10 µL of extraction solvent. Next, the tissue samples were homogenized using the Dounce homogenizer. After the homogenization, 200 µL of homogenate was mixed with 640 µL of MeOH and 160 µL of Methyl-Tert-Butyl ether (MTBE) to extract hydrophobic compounds. Samples were then vortex-mixed for 1 hour at room temperature (RT) and centrifuged at 4000 g for 20 min at 20°C. The samples were then passed through spin X columns (0.22 µm filter), and 200 µL of the filtered sample was dried at RT in the vacuum concentrator. From here, the samples were sent to CEMBIO for the UHPLC-MS analysis. Prior to the analysis, dried samples were re-suspended with 200 µL of MeOH/MTBE/H2O (7.4:1.6:1, v/v/v), which contained the corresponding ISs (C17 – sphingosine at 1 ppm for positive ion mode, and d31–palmitic acid at 3 ppm for negative ion mode). Samples were then centrifuged (16,100xg, 5 min, 15°C) before transferring them into sample vials with glass inserts for LC-MS analysis.