Dataset - Proteomics High-density Lipoprotein (HDL) Structure and Function Proteomics (JM-DP1)

Dataset Description

The purpose of this experiment was to investigate how the interactions between APOA1 and APOA2 on the surface of high-density lipoproteins (HDL) impact particle function. Interactions were investigated on HDL isolated from human blood plasma using structural proteomics tools such as chemical cross-linking and limited proteolysis (LiP). The structural proteomics data was acquired using a Q-Exactive HF-X mass spectrometer and processed using MaxQuant software (v.1.6.17.0). Data was further processed by RomicsProcessor.

Data Download Reference Citations

1. Sarkar, Snigdha, et al. PPI DataHub Project Data Package: High-density Lipoprotein (HDL) Structure and Function Proteomics. United States. 2024. PNNL DataHub (Web). DOI: 10.25584/PPI/2447854
2. Sarkar S, Morris J, You Y, Sexmith H, Street SE, Thibert SM, Attah IK, Hutchinson Bunch CM, Novikova IV, Evans JE, Shah AS, Gordon SM, Segrest JP, Bornfeldt KE, Vaisar T, Heinecke JW, Davidson WS, Melchior JT. APOA2 increases cholesterol efflux capacity to plasma HDL by displacing the C-terminus of resident APOA1. J Lipid Res. 2024 Dec;65(12):100686. doi: 10.1016/j.jlr.2024.100686. Epub 2024 Oct 28. PMID: 39490930; PMCID: PMC11617996.

Accessible Digital Data Downloads

The repository contains the following folders and files:

• JM-DP1_SampleMetadata.xlsx: Contains sample metadata information including descriptors, experimental conditions, cell lines (if applicable)
• JM-DP1_ExpressionData.xlsx Raw counts, normalized counts, and statistics

Total Download Size: ?? MB, zipped

Linked Primary Data

Primary liquid chromatography-mass spectrometry (LC-MS) raw measurement data are openly accessible for download at the Mass Spectrometry Interactive Virtual Environment (MassIVE) community repository under the accession MSV000095479.

Funding Acknowledgments

The research data described here was funded in whole or in part by the Predictive Phenomics Initiative (PPI) at Pacific Northwest National Laboratory (PNNL). This work was conducted under the Laboratory Directed Research and Development Program at PNNL. A portion of this research was performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy (DOE) Office of Science located at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the DOE under Contract No. DE-AC05-76RL01830.

Citation Policy

In efforts to enable discovery, reproducibility, and reuse of PPI-funded project dataset citations in accordance with best practices (as outlined by the FORCE11 Data Citation Principles), we ask that all reuse of project data and metadata download materials acknowledge all primary and secondary dataset citations and corresponding journal articles where applicable.

Data Licensing

Creative Commons Attribution 4.0 International (CC BY 4.0)