A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

Tue Bjerg Bennike; Melena D. Bellin; Yue Xuan; Allan Stensballe; Frederik Trier Møller; Gregory J. Beilman; Ofer Levy; Zobeida Cruz-Monserrate; Vibeke Andersen; Judith Steen; Darwin L. Conwell; Hanno Steen

doi:10.1021/acs.jproteome.8b00111

A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

Tue Bjerg Bennike, Melena D. Bellin, Yue Xuan, Allan Stensballe, Frederik Trier Møller, Gregory J. Beilman, Ofer Levy, Zobeida Cruz-Monserrate, Vibeke Andersen, Judith Steen, Darwin L. Conwell, Hanno Steen

Internal Medicine

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.

Original language	English
Pages (from-to)	1983-1992
Number of pages	10
Journal	Journal of Proteome Research
Volume	17
Issue number	5
DOIs	https://doi.org/10.1021/acs.jproteome.8b00111
State	Published - May 4 2018

Bibliographical note

Funding Information:
O.L. and H.S.’s laboratories are supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Human Immunology Project Consortium (HIPC) Award Number U19AI118608. The research reported in this publication was also supported by the National Cancer Institute and National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) under award number U01DK108327 (H.S., D.C.). M.D.B.’s laboratory was supported by grants from the American Diabetes Association (1-11-CT-06) and the National Institutes of Health (K23 DK084315). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Furthermore, we acknowledge the following grants that enabled the work described in this manuscript: T.B.B., funding from the Lundbeck Foundation (R181-2014-3372 and R275-2017-2219), The Carlsberg Foundation (CF14-0561), and A. P. Mølle; A.S., funding from the Obelske Family Foundation, the Svend Andersen Foundation, the Spar Nord Foundation, and the Danish National Mass Spectrometry Platform for Functional Proteomics (PRO-MS); and V.A., funding from the Lundbeck Foundation (R126-2012-12194), Hospital of Southern Jutland, University of Southern Denmark, and “Knud og Edith Eriksens Mindefond”.

Publisher Copyright:
© Copyright 2018 American Chemical Society.

Keywords

TPIAT
biomarker
data-independent acquisition
plasma
serum

ASJC Scopus subject areas

Biochemistry
Chemistry (all)

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10.1021/acs.jproteome.8b00111

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Bennike, T. B., Bellin, M. D., Xuan, Y., Stensballe, A., Møller, F. T., Beilman, G. J., Levy, O., Cruz-Monserrate, Z., Andersen, V., Steen, J., Conwell, D. L., & Steen, H. (2018). A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation. Journal of Proteome Research, 17(5), 1983-1992. https://doi.org/10.1021/acs.jproteome.8b00111

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title = "A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation",

abstract = "Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.",

keywords = "TPIAT, biomarker, data-independent acquisition, plasma, serum",

author = "Bennike, {Tue Bjerg} and Bellin, {Melena D.} and Yue Xuan and Allan Stensballe and M{\o}ller, {Frederik Trier} and Beilman, {Gregory J.} and Ofer Levy and Zobeida Cruz-Monserrate and Vibeke Andersen and Judith Steen and Conwell, {Darwin L.} and Hanno Steen",

note = "Funding Information: O.L. and H.S.{\textquoteright}s laboratories are supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Human Immunology Project Consortium (HIPC) Award Number U19AI118608. The research reported in this publication was also supported by the National Cancer Institute and National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) under award number U01DK108327 (H.S., D.C.). M.D.B.{\textquoteright}s laboratory was supported by grants from the American Diabetes Association (1-11-CT-06) and the National Institutes of Health (K23 DK084315). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Furthermore, we acknowledge the following grants that enabled the work described in this manuscript: T.B.B., funding from the Lundbeck Foundation (R181-2014-3372 and R275-2017-2219), The Carlsberg Foundation (CF14-0561), and A. P. M{\o}lle; A.S., funding from the Obelske Family Foundation, the Svend Andersen Foundation, the Spar Nord Foundation, and the Danish National Mass Spectrometry Platform for Functional Proteomics (PRO-MS); and V.A., funding from the Lundbeck Foundation (R126-2012-12194), Hospital of Southern Jutland, University of Southern Denmark, and “Knud og Edith Eriksens Mindefond”. Publisher Copyright: {\textcopyright} Copyright 2018 American Chemical Society.",

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doi = "10.1021/acs.jproteome.8b00111",

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Bennike, TB, Bellin, MD, Xuan, Y, Stensballe, A, Møller, FT, Beilman, GJ, Levy, O, Cruz-Monserrate, Z, Andersen, V, Steen, J, Conwell, DL & Steen, H 2018, 'A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation', Journal of Proteome Research, vol. 17, no. 5, pp. 1983-1992. https://doi.org/10.1021/acs.jproteome.8b00111

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T1 - A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

AU - Bennike, Tue Bjerg

AU - Bellin, Melena D.

AU - Xuan, Yue

AU - Stensballe, Allan

AU - Møller, Frederik Trier

AU - Beilman, Gregory J.

AU - Levy, Ofer

AU - Cruz-Monserrate, Zobeida

AU - Andersen, Vibeke

AU - Steen, Judith

AU - Conwell, Darwin L.

AU - Steen, Hanno

N1 - Funding Information: O.L. and H.S.’s laboratories are supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Human Immunology Project Consortium (HIPC) Award Number U19AI118608. The research reported in this publication was also supported by the National Cancer Institute and National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) under award number U01DK108327 (H.S., D.C.). M.D.B.’s laboratory was supported by grants from the American Diabetes Association (1-11-CT-06) and the National Institutes of Health (K23 DK084315). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Furthermore, we acknowledge the following grants that enabled the work described in this manuscript: T.B.B., funding from the Lundbeck Foundation (R181-2014-3372 and R275-2017-2219), The Carlsberg Foundation (CF14-0561), and A. P. Mølle; A.S., funding from the Obelske Family Foundation, the Svend Andersen Foundation, the Spar Nord Foundation, and the Danish National Mass Spectrometry Platform for Functional Proteomics (PRO-MS); and V.A., funding from the Lundbeck Foundation (R126-2012-12194), Hospital of Southern Jutland, University of Southern Denmark, and “Knud og Edith Eriksens Mindefond”. Publisher Copyright: © Copyright 2018 American Chemical Society.

PY - 2018/5/4

Y1 - 2018/5/4

N2 - Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.

AB - Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.

KW - TPIAT

KW - biomarker

KW - data-independent acquisition

KW - plasma

KW - serum

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UR - http://www.scopus.com/inward/citedby.url?scp=85046679050&partnerID=8YFLogxK

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VL - 17

SP - 1983

EP - 1992

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ER -

A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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