Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery

Area of Science:

• Proteomics and Mass Spectrometry
• Clinical Biomarker Discovery
• Biofluid Analysis

Background:

• Plasma proteomics is vital for identifying disease biomarkers.
• Commercial plasma is frequently used for proteomic research and controls.
• Assumed consistency in plasma preparation across commercial sources is common.

Purpose of the Study:

• To evaluate a particle-based protein enrichment strategy versus conventional methods for plasma proteomics.
• To investigate variability in plasma proteomes from commercial sources.
• To identify sources of variability, including sample handling and processing.

Main Methods:

• Plasma samples from five commercial sources were analyzed.
• Particle-based enrichment and conventional workflows were compared.
• Data-independent acquisition mass spectrometry was performed on two instruments (Exploris 480, timsTOF HT) using CHIMERYS and DIA-NN algorithms.

Main Results:

• Particle-based enrichment yielded 2.8- to 6.2-fold more proteins than conventional methods, exceeding 5000 proteins on the timsTOF HT.
• Variability in plasma proteome composition was primarily linked to differences in whole blood-to-plasma processing procedures.
• Procedural differences, undetectable by conventional workflows, were revealed by particle-dependent proteome profiling.

Conclusions:

• Standard operating procedures for plasma preparation significantly impact proteomic profiles.
• Particle-based enrichment is a more sensitive method for detecting subtle proteomic variations.
• Careful consideration of sample source and preparation is essential for reliable plasma proteomics and biomarker studies.