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.
| Study ID | ST002849 |
| Study Title | Lipidomics for unlinked CD1 proteins |
| Study Summary | In 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 Name | Huang |
| First Name | Shouxiong |
| Address | 251 Kettering Laboratory Complex, 160 Panzeca Way, Cincinnati, OH |
| shouxiong.huang@uc.edu | |
| Phone | 5135587572 |
| Submit Date | 2023-08-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzdata.xml |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
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 |
|---|---|---|
| SA308574 | H2O-3 | Blank control |
| SA308575 | H2O-2 | Blank control |
| SA308576 | H2O-1 | Blank control |
| SA308577 | NIHCD1a-3 | CD1a |
| SA308578 | NIHCD1a-2 | CD1a |
| SA308579 | NIHCD1a-1 | CD1a |
| SA308580 | NIHCD1b-3 | CD1b |
| SA308581 | NIHCD1b-2 | CD1b |
| SA308582 | NIHCD1b-1 | CD1b |
| SA308583 | NIHCD1c-3 | CD1c |
| SA308584 | NIHCD1c-1 | CD1c |
| SA308585 | NIHCD1c-2 | CD1c |
| SA308586 | NIHCD1d-1 | CD1d |
| SA308587 | NIHCD1d-3 | CD1d |
| SA308588 | NIHCD1d-2 | CD1d |
| SA308589 | NIHMamu-3 | Mamu control |
| SA308590 | NIHMamu-1 | Mamu control |
| SA308591 | NIHMamu-2 | Mamu 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 |
