Analysis of 1508 plasma samples by capillary-flow data-independent acquisition profiles proteomics of weight loss and maintenance
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Analysis of 1508 plasma samples by capillary-flow data-independent acquisition profiles proteomics of weight loss and maintenance. / Bruderer, Roland; Muntel, Jan; Müller, Sebastian; Bernhardt, Oliver M; Gandhi, Tejas; Cominetti, Ornella; Macron, Charlotte; Carayol, Jérôme; Rinner, Oliver; Astrup, Arne; Saris, Wim H M; Hager, Jorg; Valsesia, Armand; Dayon, Loïc; Reiter, Lukas.
In: Molecular and Cellular Proteomics, Vol. 18, No. 6, 2019, p. 1242-1254.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Analysis of 1508 plasma samples by capillary-flow data-independent acquisition profiles proteomics of weight loss and maintenance
AU - Bruderer, Roland
AU - Muntel, Jan
AU - Müller, Sebastian
AU - Bernhardt, Oliver M
AU - Gandhi, Tejas
AU - Cominetti, Ornella
AU - Macron, Charlotte
AU - Carayol, Jérôme
AU - Rinner, Oliver
AU - Astrup, Arne
AU - Saris, Wim H M
AU - Hager, Jorg
AU - Valsesia, Armand
AU - Dayon, Loïc
AU - Reiter, Lukas
N1 - CURIS 2019 NEXS 189 Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - Faculty of Science
KW - Plasma proteomics
KW - Data-independent acquisition
KW - SWATH
KW - Label-free quantification
KW - Stable isotope-based quantification
KW - Library
KW - Single shot
KW - High throughput
KW - clinical proteomics
U2 - 10.1074/mcp.RA118.001288
DO - 10.1074/mcp.RA118.001288
M3 - Journal article
C2 - 30948622
VL - 18
SP - 1242
EP - 1254
JO - Molecular and Cellular Proteomics
JF - Molecular and Cellular Proteomics
SN - 1535-9476
IS - 6
ER -
ID: 216206215