Systematic evaluation of the use of human plasma and serum for mass-spectrometry-based shotgun proteomics

Document Type

Journal Article

Publication Title

Journal of Proteome Research


American Chemical Society


School of Medical and Health Sciences / Centre of Excellence for Alzheimer’s Disease Research and Care




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.


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.



Access Rights

subscription content