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

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Resumé

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.

OriginalsprogEngelsk
TidsskriftJournal of Proteome Research
Vol/bind17
Udgave nummer5
Sider (fra-til)1983–1992
ISSN1535-3893
DOI
StatusUdgivet - 4. maj 2018

Fingeraftryk

Pancreatectomy
Workflow
Throughput
Plasmas
Chronic Pancreatitis
Biomarkers
Serum
Costs
Plasma Volume
Body fluids
Liquid chromatography
Proteome
Liquid Chromatography
Surgery
Mass spectrometry
Blood Proteins
Blood
Membranes
Proteomics
Monitoring

Citer dette

Bennike, Tue Bjerg ; Bellin, Melena D ; Xuan, Yue ; Stensballe, Allan ; Trier Møller, Frederik ; Beilman, Gregory J ; Levy, Ofer ; Cruz-Monserrate, Zobeida ; Andersen, Vibeke ; Steen, Judith ; Conwell, Darwin L ; Steen, Hanno. / A cost-effective high throughput plasma and serum proteomics workflow enables mapping of the molecular impact of total pancreatectomy with islet autotransplantation. I: Journal of Proteome Research. 2018 ; Bind 17, Nr. 5. s. 1983–1992.
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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.",
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author = "Bennike, {Tue Bjerg} and Bellin, {Melena D} and Yue Xuan and Allan Stensballe and {Trier M{\o}ller}, Frederik and Beilman, {Gregory J} and Ofer Levy and Zobeida Cruz-Monserrate and Vibeke Andersen and Judith Steen and Conwell, {Darwin L} and Hanno Steen",
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Bennike, TB, Bellin, MD, Xuan, Y, Stensballe, A, Trier Møller, F, 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, bind 17, nr. 5, s. 1983–1992. https://doi.org/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. / Bennike, Tue Bjerg; Bellin, Melena D; Xuan, Yue; Stensballe, Allan; Trier Møller, Frederik; Beilman, Gregory J; Levy, Ofer; Cruz-Monserrate, Zobeida; Andersen, Vibeke; Steen, Judith; Conwell, Darwin L; Steen, Hanno.

I: Journal of Proteome Research, Bind 17, Nr. 5, 04.05.2018, s. 1983–1992.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

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 - Trier Møller, Frederik

AU - Beilman, Gregory J

AU - Levy, Ofer

AU - Cruz-Monserrate, Zobeida

AU - Andersen, Vibeke

AU - Steen, Judith

AU - Conwell, Darwin L

AU - Steen, Hanno

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

KW - Humans

KW - Pancreatectomy

KW - Pancreatitis

KW - Transplantation, Autologous

KW - Workflow

KW - Blood Proteins/analysis

KW - Tandem Mass Spectrometry

KW - Cost-Benefit Analysis

KW - Chromatography, Liquid

KW - Islets of Langerhans Transplantation

KW - Proteomics/methods

KW - Biomarkers/blood

U2 - 10.1021/acs.jproteome.8b00111

DO - 10.1021/acs.jproteome.8b00111

M3 - Journal article

VL - 17

SP - 1983

EP - 1992

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 5

ER -