Analysis of 1508 plasma samples by capillary-flow data-independent acquisition profiles proteomics of weight loss and maintenance

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Roland Bruderer, Jan Muntel, Sebastian Müller, Oliver M Bernhardt, Tejas Gandhi, Ornella Cominetti, Charlotte Macron, Jérôme Carayol, Oliver Rinner, Arne Astrup, Wim H M Saris, Jorg Hager, Armand Valsesia, Loïc Dayon, Lukas Reiter

Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies (1, 2), we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform is capable of measuring 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1,508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. 564 proteins (459 identified with two or more peptide sequences) were profiled with 74% dataset completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% dataset completeness with CVs for protein measurements of 10.9%.The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other large-scale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of non-enzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA.In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.

Original languageEnglish
JournalMolecular and Cellular Proteomics
Volume18
Issue number6
Pages (from-to)1242-1254
Number of pages13
ISSN1535-9476
DOIs
Publication statusPublished - 2019

    Research areas

  • The Faculty of Science - Plasma proteomics, Data-independent acquisition, SWATH, Label-free quantification, Stable isotope-based quantification, Library, Single shot, High throughput, clinical proteomics

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