Systematic evaluation of the use of human plasma and serum for mass-spectrometry-based shotgun proteomics
Abstract
Over the last two decades, EDTA-plasma has been used as the preferred sample matrix for human blood proteomic profiling. Serum has also been employed widely. Only a few studies have assessed the difference and relevance of the proteome profiles obtained from plasma samples, such as EDTA-plasma or lithium-heparin-plasma, and serum. A more complete evaluation of the use of EDTA-plasma, heparin-plasma, and serum would greatly expand the comprehensiveness of shotgun proteomics of blood samples. In this study, we evaluated the use of heparin-plasma with respect to EDTA-plasma and serum to profile blood proteomes using a scalable automated proteomic pipeline (ASAP2). The use of plasma and serum for mass-spectrometry-based shotgun proteomics was first tested with commercial pooled samples. The proteome coverage consistency and the quantitative performance were compared. Furthermore, protein measurements in EDTA-plasma and heparin-plasma samples were comparatively studied using matched sample pairs from 20 individuals from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Study. We identified 442 proteins in common between EDTA-plasma and heparin-plasma samples. Overall agreement of the relative protein quantification between the sample pairs demonstrated that shotgun proteomics using workflows such as the ASAP2 is suitable in analyzing heparin-plasma and that such sample type may be considered in large-scale clinical research studies. Moreover, the partial proteome coverage overlaps (e.g., ∼70%) showed that measures from heparin-plasma could be complementary to those obtained from EDTA-plasma.
Keywords
EDTA, heparin, mass spectrometry, plasma, serum, shotgun proteomics
Document Type
Journal Article
Date of Publication
2018
Publication Title
Journal of Proteome Research
Publisher
American Chemical Society
School
School of Medical and Health Sciences / Centre of Excellence for Alzheimer’s Disease Research and Care
RAS ID
27575
Copyright
subscription content
Comments
Lan, J., Núñez Galindo, A., Doecke, J., Fowler, C., Martins, R. N., Rainey-Smith, S. R., ... & Dayon, L. (2018). Systematic evaluation of the use of human plasma and serum for mass-spectrometry-based shotgun proteomics. Journal of Proteome Research, 17(4), 1426-1435. Available here.