GNPS Smoke Inhalation and NIST SRM Lipidomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 6560 Q-TOF LC/MS
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Erin Baker
PROVIDER: MSV000088372 | GNPS | Fri Nov 12 08:12:00 GMT 2021
REPOSITORIES: GNPS
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Project description:LC-IMS-CID-MS lipidomics of BALF and plasma from severe smoke inhalation and NIST SRM 1950.
2021-11-12 | MSV000088372 | MassIVE
Project description:Lipids in the reference material NIST SRM 1950 (50 uL) were extracted according to the Matyash protocol. The sample was analysed in 5 technical replicates by ESI(-)-HILIC-TIMS-MS with PASEF enabled with 100 ms.
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Project description:As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each laboratory using a different lipidomics workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and interlaboratory quality control and method validation. These analyses were performed using nonstandardized laboratory-independent workflows. The consensus locations were also compared with a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement.
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Project description:<p>Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.</p><p><br></p><p>In MTBLS1375, to validate tissue-specific transitions which we generated with LipidCreator, we conducted quantitative lipidomics experiments monitoring 433 lipids in the plasma of 21 healthy Asian human subjects. For a subset of 50 individual lipid levels the concentrations were compared to a recently conducted ring trial monitoring the lipid content of a reference material obtained from a mixed American population (NIST SRM 1950). The rationale behind this was to see if the creation of a list including internal standard and endogenous lipids lead to similar quantitative results as the ring trial experiment.</p><p><br></p><p>Studies linked to this manuscript include;</p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1333' rel='noopener noreferrer' target='_blank'>MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HF</a></p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1334' rel='noopener noreferrer' target='_blank'>MTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTof</a></p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1369' rel='noopener noreferrer' target='_blank'>MTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1375' rel='noopener noreferrer' target='_blank'>MTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard</a></p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1376' rel='noopener noreferrer' target='_blank'>MTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identification</a></p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1381' rel='noopener noreferrer' target='_blank'>MTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS1382' rel='noopener noreferrer' target='_blank'>MTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation</a></p>
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Project description:This study is a test of the untargeted metabolomics approach to studying samples from exposure studies. The samples are NIST standard SRM 3672 for pooled urine of smokers and SRM 3673 for pooled urine of non-smokers. A broad spectrum GCMS approach was used in this study.
2016-06-10 | ST000420 | MetabolomicsWorkbench
Project description:The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) in collaboration with the National Institute of Standards (NIST) recently produced a human plasma standard reference material (SRM 1950) for metabolite analysis. The SRM was prepared by obtaining plasma samples from 100 individuals between 40 and 50 years of age, whose ethnicity was representative of the US population and that included an equal number of men and women. The intent of the NIDDK/NIST project was to provide a reference material that would be publically available to researchers and that could be used by the clinical chemistry community to identify plasma metabolites for diagnostic purposes. Signature metabolites could then be further probed for their usefulness as disease biomarkers. The LIPID MAPS Consortium has undertaken the task to analyze this SRM by systematically identifying and quantifying the lipid molecular species in the six main categories of mammalian lipids. The quantitative levels of over 500 different lipids present in this reference human plasma sample are presented here.
2013-02-20 | ST000004 | MetabolomicsWorkbench
Project description:Lipids in the reference material NIST 1950 (50 uL) were extracted accodring to the Matyash protocol. The sample was analysed in 5 technical replicates by ESI(-)-HILIC-TIMS-MS with PASEF enabled with 100 ms and 500 ms.
2022-11-30 | MSV000090817 | MassIVE
Project description:Lipids in the reference material NIST SRM 1950 (50 uL) were extracted according to the Matyash protocol. The sample was analysed in 5 technical replicates by ESI(-)-HILIC-TIMS-MS with PASEF enabled with 100 ms.
2022-12-09 | MSV000090873 | GNPS
Project description:This dataset contains lipidomics data of NIST SRM 1950 plasma acquired by the three-fold approach: capillary LC/nanoelectrospray for enhanced ionization, QLT for higher sensitivity, and maximized parallelization of mass analyzers for efficient acquisition.
2022-01-27 | MSV000088741 | MassIVE
Project description:GNPS - NIST 1950 Serum SRM serial dilution processed with MZmine2 and OpenMS for Feature Based Molecular Networking. Files were obtained from the MSV000081364 (GNPS - NIST Standard Reference Material Human Serum - Column Comparability) https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=010ce4f32b1d4c56aff9402d370d0c15 NIST SRM-1950 was processed using an 80% EtOH extraction protocol (found here 10.1021/ac402503m) and subsequently ran on a UHPLC using a Phenomenex Luna 1.6u C18 Polar Data coupled to Q Exactive Orbtirap (Thermo Fisher Scientific). Files were converted from mzXML to mzML with MSConvert.
2019-07-15 | MSV000084092 | GNPS