Strategies for consistent and automated quantification of HDL proteome using data-independent acquisition.

ABSTRACT: The introduction of mass spectrometry-based proteomics has revolutionized the high-density lipoprotein (HDL) field, with the description, characterization, and implication of HDL-associated proteins in an array of pathologies. However, acquiring robust, reproducible data is still a challenge in the quantitative assessment of HDL proteome. Data-independent acquisition (DIA) is a mass spectrometry methodology that allows the acquisition of reproducible data, but data analysis remains a challenge in the field. To date, there is no consensus on how to process DIA-derived data for HDL proteomics. Here, we developed a pipeline aiming to standardize HDL proteome quantification. We optimized instrument parameters and compared the performance of four freely available, user-friendly software tools (

SUBMITTER: Souza Junior DR 

PROVIDER: S-EPMC10339053 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature