Evaluation of Blood-Based Sample Types for Deep Plasma Proteomics
This application note explores how deep and unbiased proteomics analysis reveals differences between serum and plasma proteomes.
New technologies to identify and assess proteins are allowing plasma proteomics biomarker studies to be conducted at greater depth and scale than ever before. Sample collection and processing methods are important for ensuring accurate results from a large cohort study. To evaluate the relative differences and potential advantages of blood-based sample types for large cohort LC-MS based proteomics studies, we compared three sample types: serum, EDTA-plasma, and citrate-plasma. Our results show significantly deeper proteome coverage using Seer’s proprietary engineered nanoparticle based ProteographTM workflow compared to a traditional neat sample digestion workflow. This deeper proteome coverage revealed significant differences between these three blood-based sample types. Therefore, we recommend using a single sample type following the same collection protocol for large cohort studies to minimize the impact of sample collection and processing differences.
Introduction
Serum and plasma are common blood-based sample types used for biomarker discovery studies. While these sample types are similar, the abundance of proteins could be altered depending on the method of collection and processing. Proteomics analysis provides valuable insight to explain complex biology, but it remains challenging to collect deep proteome coverage at the scale necessary for large cohort studies. To determine if significant differences or advantages exist between sample types, we undertook this study to characterize the differences between serum and plasma proteomes and assess their suitability for large-scale, unbiased, protein biomarker discovery studies.
We collected matched serum and plasma from 15 individual donors and processed them with the Seer Proteograph workflow. Both peptides and protein group identification performance using LC-MS analysis were evaluated in this study. This application note will explore how deep and unbiased proteomics analysis reveals differences between the serum and plasma proteomes.
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