Summary of Study ST002849

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 PR001783. The data can be accessed directly via it's Project DOI: 10.21228/M87M7X 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.

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Study IDST002849
Study TitleLipidomics for unlinked CD1 proteins
Study SummaryIn study 4217, the four types of human CD1 antigen-presenting molecules were constructed using a peptide zipper between heavy chains of CD1 proteins and beta 2 macroglobulin (B2m), thus called unlinked CD1 proteins, expressed in human embryonic kidney cell line HEK293T cells, purified using affinity chromatography, and extracted using the adapted Folch method for bound lipids. These extracted lipids in triplicates from four CD1 proteins were profiled using the extraction from in parallel generated MamuA01 protein (MHC protein from the rhesus monkey Macaca mulatta) as a control. The four types of human CD1 antigen presenting molecules show differing lipid capture motifs based on the length and chemical structures of lipids bound, pointing to general self-lipid capture mechanisms. For CD1a and CD1d, lipid size matches CD1 cleft volume, whereas CD1b shows a nearly universal size mismatch with its ligands, which results from the uniform seating of two small lipids within its large cleft. Further, the list of compounds that comprise the assembled CD1 lipidomes provides a resource for matching to bioactive lipids from other fields of research and supports the ongoing discovery of lipid blockers and antigens for T cells.
Institute
Brigham and Women's Hospital
Last NameHuang
First NameShouxiong
Address251 Kettering Laboratory Complex, 160 Panzeca Way, Cincinnati, OH
Emailshouxiong.huang@uc.edu
Phone5135587572
Submit Date2023-08-10
Raw Data AvailableYes
Raw Data File Type(s)mzdata.xml
Analysis Type DetailLC-MS
Release Date2023-11-10
Release Version1
Shouxiong Huang Shouxiong Huang
https://dx.doi.org/10.21228/M87M7X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001783
Project DOI:doi: 10.21228/M87M7X
Project Title:Lipidomics for linked and unlinked CD1 proteins
Project Summary:The cellular CD1 system binds lipid antigens for display to T cells. Here we developed a lipidomics platform that detected > 2000 distinct lipids in cellular CD1 complexes, demonstrating a broad display of self-sphingolipids and phospholipids to T cells. The four types of human CD1 antigen presenting molecules show differing lipid capture motifs based on the length and chemical structures of lipids bound, pointing to general self-lipid capture mechanisms. For CD1a and CD1d, lipid size matches CD1 cleft volume, whereas CD1b shows a nearly universal size mismatch with its ligands, which results from the uniform seating of two small lipids within its large cleft. Further, the list of compounds that comprise the assembled CD1 lipidomes provides a resource for matching to bioactive lipids from other fields of research and supports the ongoing discovery of lipid blockers and antigens for T cells.
Institute:Brigham and Women's Hospital
Last Name:Huang
First Name:Shouxiong
Address:251 Kettering Laboratory Complex, 160 Panzeca Way, Cincinnati, OH
Email:shouxiong.huang@uc.edu
Phone:5135587572

Subject:

Subject ID:SU002961
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Proteins bound with detected lipids
SA308574H2O-3Blank control
SA308575H2O-2Blank control
SA308576H2O-1Blank control
SA308577NIHCD1a-3CD1a
SA308578NIHCD1a-2CD1a
SA308579NIHCD1a-1CD1a
SA308580NIHCD1b-3CD1b
SA308581NIHCD1b-2CD1b
SA308582NIHCD1b-1CD1b
SA308583NIHCD1c-3CD1c
SA308584NIHCD1c-1CD1c
SA308585NIHCD1c-2CD1c
SA308586NIHCD1d-1CD1d
SA308587NIHCD1d-3CD1d
SA308588NIHCD1d-2CD1d
SA308589NIHMamu-3Mamu control
SA308590NIHMamu-1Mamu control
SA308591NIHMamu-2Mamu control
Showing results 1 to 18 of 18

Collection:

Collection ID:CO002954
Collection Summary:Lipidomic profiles were generated from lipids that were extracted from HEK293T-expressed CD1a, CD1b, CD1c, and CD1d proteins compared with peptide-binding protein MamuA01 and H2O blank controls.
Sample Type:HEK cells

Treatment:

Treatment ID:TR002970
Treatment Summary:Lipidomic profiles were generated from lipids that were extracted from HEK293T-expressed CD1a, CD1b, CD1c, and CD1d proteins compared with peptide-binding protein MamuA01 and H2O blank controls. No other treatment was applied.
Treatment Protocol Filename:CD1_lipidomics-090523.docx

Sample Preparation:

Sampleprep ID:SP002967
Sampleprep Summary:Lipidomic profiles were generated from lipids that were extracted from HEK293T-expressed CD1a, CD1b, CD1c, and CD1d proteins compared with peptide-binding protein MamuA01 and H2O blank controls. No other treatment was applied. See protocol file for details.
Sampleprep Protocol Filename:CD1_lipidomics-090523.docx

Combined analysis:

Analysis ID AN004667
Analysis type MS
Chromatography type Normal phase
Chromatography system Agilent 1200
Column First through a MetaGuard guard column (2 mm, 3 μm, Varian, A0542-MG2) and then a MonoChrom Diol column (150 X 2 mm, 3μm, Varian, A0542150X020)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6520 QTOF
Ion Mode POSITIVE
Units 631

Chromatography:

Chromatography ID:CH003513
Chromatography Summary:Triplicate samples for each protein analyzed with blanks that were intermixed and monitored for lipid carryover, using an Agilent 1200 series HPLC autosampler with an Agilent 6520 Accurate-Mass Q-TOF MS controlled by MassHunter software. See methods/protocol file for details.
Methods Filename:CD1_lipidomics-090523.docx
Instrument Name:Agilent 1200
Column Name:First through a MetaGuard guard column (2 mm, 3 μm, Varian, A0542-MG2) and then a MonoChrom Diol column (150 X 2 mm, 3μm, Varian, A0542150X020)
Column Temperature:22
Flow Gradient:The binary gradient was monitored with solvent B with 100% at 0-10 min, 50% at 17-22 min, 0% at 30-35 min, and 100% at 40-50 min, followed by an additional 0% for 6 min post-run for regeneration.
Flow Rate:0.7 ml/min
Solvent A:70% isopropanol, 30% methanol, 0.1% formic acid, and 0.05% ammonium hydroxide
Solvent B:70% hexanes, 30% isopropanol, 0.1% formic acid, and 0.05% ammonium hydroxide
Chromatography Type:Normal phase

MS:

MS ID:MS004414
Analysis ID:AN004667
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS data were acquired with MassHunter software. See Analysis protocol file for details.
Ion Mode:POSITIVE
Analysis Protocol File:CD1_lipidomics-090523.docx
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