Dataset - Proteomics LiP-MS and Chemical Cross-Linking to Assess Structural Impact of APOA2 on human High-density Lipoproteins (HDL) (JM-DP1)

Dataset Description

This dataset investigates how interactions between APOA1 and APOA2 on the surface of human high-density lipoproteins (HDL) may influence particle structure and function. HDL was isolated from human blood plasma and exposed to exogenous APOA2. Structural proteomics measurements were performed using limited proteolysis (LiP) and chemical cross-linking coupled to mass spectrometry. Data were acquired on a Q Exactive HF-X mass spectrometer and processed using MaxQuant (v.1.6.17.0).

Data Download Reference Citations

• Sarkar, Snigdha, Katrina M Waters and John Melchior. 2024. High-density Lipoprotein (HDL) Structure and Function Proteomics (JM-DP1). 2024. https://doi.org/10.25584/PPI/2447854   

Accessible Digital Data Downloads

The repository contains the following folders and files:

• JM-DP1_SampleMetadata.xlsx: Contains sample metadata information including descriptors, experimental conditions, and sample processing
• JM-DP1_APOA2 LIP data.xlsx Normalized intensities, statistics and protein structural changes

Total Download Size: 828KB

Linked Publications

• 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.

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)