An Optimized Data-Independent Acquisition Strategy for Comprehensive Analysis of Human Plasma Proteome.

Haoyun Fang; David W Greening
Abstract
Cartography of the plasma proteome remains technically challenging, primarily due to the abundance and dynamic range of plasma proteins and their concentrations, exceeding ten orders of magnitude, including low-abundant tissue-derived proteins in the pg/mL range. Data-independent acquisition mass spectrometry (DIA-MS) has seen advances in unbiased mass spectrometry-based proteomic analysis of the plasma proteome. Here, we describe a comprehensive proteomic workflow of human plasma from clinically relevant sample (10 μL) that includes anti-protein immunodepletion and highly sensitive sample preparation workflow, with optimized scheduled isolation DIA-MS and deep learning analysis. This approach results in over 960 proteins quantified from a single-shot analysis of broad dynamic range, across 8 orders of magnitude (8.2 ng/L to 0.67 g/L). We further compare data-dependent acquisition (DDA) MS to highlight the advantage in protein quantification and inter-sample variation. These developments have provided streamlined identification of the human plasma proteome, including low-abundant tissue-enriched proteins, and applications toward understanding the plasma proteome.
Journal METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.)
ISSN 1940-6029
Published 01 Jan 2023
Volume 2628
Issue
Pages 93 107 93-107
DOI 10.1007/978-1-0716-2978-9_7
Type Journal Article
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