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.