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

J. Lan; A. Núñez Galindo; J. Doecke; C. Fowler; R.N. Martins; S.R. Rainey-Smith; O. Cominetti; L. Dayon

doi:10.1021/acs.jproteome.7b00788

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

Journal article

Peer reviewed

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

J. Lan, A. Núñez Galindo, J. Doecke, C. Fowler, R.N. Martins, S.R. Rainey-Smith, O. Cominetti and L. Dayon

Journal of Proteome Research, Vol.17(4), pp.1426-1435

2018

DOI: https://doi.org/10.1021/acs.jproteome.7b00788

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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.

Details

Title: Systematic evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics
Authors/Creators: J. Lan (Author/Creator) - Nestlé
A. Núñez Galindo (Author/Creator)
J. Doecke (Author/Creator) - CSIRO Health and Biosecurity/Australian E-Health Research Centre , Brisbane , Queensland 4029 , Australia.
C. Fowler (Author/Creator) - Florey Institute of Neuroscience and Mental Health
R.N. Martins (Author/Creator) - Edith Cowan University
S.R. Rainey-Smith (Author/Creator)
O. Cominetti (Author/Creator) - Nestlé
L. Dayon (Author/Creator) - Nestlé
Publication Details: Journal of Proteome Research, Vol.17(4), pp.1426-1435
Publisher: American Chemical Society
Identifiers: 991005542942407891
Copyright: © 2018 American Chemical Society
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 2 Chemistry; 2.211 Mass Spectrometry; 2.211.497 Proteomics Mass Spectrometry
Web Of Science research areas: Biochemical Research Methods
ESI research areas: Biology & Biochemistry