10.1021/acs.jproteome.7b00788.s001
Jiayi Lan
Jiayi
Lan
Antonio Núñez Galindo
Antonio Núñez
Galindo
James Doecke
James
Doecke
Christopher Fowler
Christopher
Fowler
Ralph N. Martins
Ralph N.
Martins
Stephanie R. Rainey-Smith
Stephanie
R. Rainey-Smith
Ornella Cominetti
Ornella
Cominetti
Loïc Dayon
Loïc
Dayon
Systematic Evaluation
of the Use of Human Plasma and
Serum for Mass-Spectrometry-Based Shotgun Proteomics
American Chemical Society
2018
mass-spectrometry-based shotgun proteomics
AIBL
shotgun proteomics
serum
Mass-Spectrometry-Based Shotgun Proteomics
proteome coverage consistency
EDTA-plasma
profile blood proteomes
ASAP 2
sample pairs
heparin-plasma samples
2018-02-16 00:00:00
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Systematic_Evaluation_of_the_Use_of_Human_Plasma_and_Serum_for_Mass-Spectrometry-Based_Shotgun_Proteomics/5915155
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 (ASAP<sup>2</sup>). 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 ASAP<sup>2</sup> 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.