Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

作者：Hagen M. Gegner, Thomas Naake, Aurélien Dugourd, Torsten Müller, Felix Czernilofsky, Georg Kliewer, Evelyn Jäger, Barbara Helm, Nina Kunze-Rohrbach, Ursula Klingmüller, Carsten Hopf, Carsten Müller‐Tidow, Sascha Dietrich, Julio Sáez-Rodríguez, Wolfgang Huber, Rüdiger Hell, Gernot Poschet, Jeroen Krijgsveld · 发表于：Frontiers in Molecular Biosciences · 年份：2022 · DOI：10.3389/fmolb.2022.961448 · 被引用次数：47 · 研究领域：Metabolomics and Mass Spectrometry Studies、Advanced Proteomics Techniques and Applications、Molecular Biology Techniques and Applications

Metabolomic and proteomic analyses of human plasma and serum samples harbor the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implementing a unified proteomic and metabolomic approach in a clinical setting, we assessed the influence of temperature, sitting times, and centrifugation speed on the plasma and serum metabolomes and proteomes from six healthy volunteers. We used targeted metabolic profiling (497 metabolites) and data-independent acquisition (DIA) proteomics (572 proteins) on the same samples generated with well-defined pre-analytical conditions to evaluate criteria for pre-analytical SOPs for plasma and serum samples. Time and temperature showed the strongest influence on the integrity of plasma and serum proteome and metabolome. While rapid handling and low temperatures (4°C) are imperative for metabolic profiling, the analyzed proteomics data set showed variability when exposed to temperatures of 4°C for more than 2 h, highlighting the need for compromises in a combined analysis. We formalized a quality control scoring system to objectively rate sample stability and tested this score using external data sets from other pre-analytical studies. Stringent and harmoniz...