Comparing Data-Independent Acquisition and Parallel Reaction Monitoring in Their Abilities To Differentiate High-Density Lipoprotein Subclasses

Author(s)

Silva, Amanda R. M. ^[1] ; Toyoshima, Marcos T. K. ^{[2, 3]} ; Passarelli, Marisa ^{[2, 4]} ; Di Mascio, Paolo ^[1] ; Ronsein, Graziella E. ^[1]

Affiliation

^[1] Univ Sao Paulo, Inst Quim, Dept Bioquim, BR-05513970 Sao Paulo - Brazil

^[2] Univ Sao Paulo, Fac Med, Hosp Clin, Lab Lipides LIM 10, BR-01246903 Sao Paulo - Brazil

^[3] Univ Sao Paulo, Fac Med, Hosp Clin, Serv Oncoendocrinol, Inst Canc Estado Sao Paulo Oc, BR-01246000 Sao Paulo - Brazil

^[4] Univ Nove Julho, Programa Posgrad, BR-01504001 Sao Paulo - Brazil

• Document type: Journal article
• Source: JOURNAL OF PROTEOME RESEARCH; v. 19, n. 1, p. 248-259, JAN 2020.
• Web of Science Citations: 0

Abstract

High-density lipoprotein (HDL) is a diverse group of particles with multiple cardioprotective functions. HDL proteome follows HDL particle complexity. Many proteins were described in HDL, but consistent quantification of HDL protein cargo is still a challenge. To address this issue, the aim of this work was to compare data-independent acquisition (DIA) and parallel reaction monitoring (PRM) methodologies in their abilities to differentiate HDL subclasses through their proteomes. To this end, we first evaluated the analytical performances of DIA and PRM using labeled peptides in pooled digested HDL as a biological matrix. Next, we compared the quantification capabilities of the two methodologies for 24 proteins found in HDL2 and HDL3 from 19 apparently healthy subjects. DIA and PRM exhibited comparable linearity, accuracy, and precision. Moreover, both methodologies worked equally well, differentiating HDL subclasses' proteomes with high precision. Our findings may help to understand HDL functional diversity. (AU)

• FAPESP's process: 17/07725-1 - Proteomics: a tool to investigate the composition and function of HDL in hyperlipidemia
• Grantee: Amanda Ribeiro Martins da Silva
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 16/00696-3 - Proteomic as a tool to understand HDL function and composition
• Grantee: Graziella Eliza Ronsein
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 13/07937-8 - Redoxome - Redox Processes in Biomedicine
• Grantee: Ohara Augusto
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC