Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics

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.