Plasma Proteomics for Epidemiology: Increasing Throughput with Standard-Flow Rates

Xiaoke Yin; Ferheen Baig; Eloi Haudebourg; Richard T. Blankley; Tejas Gandhi; Sebastian Müller; Lukas Reiter; Helmut Hinterwirth; Raimund Pechlaner; Sotirios Tsimikas; Peter Santer; Johann Willeit; Stefan Kiechl; Joseph L. Witztum; Anthony Sullivan; Manuel Mayr

doi:10.1161/CIRCGENETICS.117.001808

Plasma Proteomics for Epidemiology: Increasing Throughput with Standard-Flow Rates

Xiaoke Yin, Ferheen Baig, Eloi Haudebourg, Richard T. Blankley, Tejas Gandhi, Sebastian Müller, Lukas Reiter, Helmut Hinterwirth, Raimund Pechlaner, Sotirios Tsimikas, Peter Santer, Johann Willeit, Stefan Kiechl, Joseph L. Witztum, Anthony Sullivan, Manuel Mayr

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Abstract

Background—Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. Methods and Results—Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS (<0.05 minutes) compared with the nanoflow LC-MS method (0.26–0.44 minutes). In addition, the standard-flow LC method also offered less variation in protein measurements. However, 5× more sample volume was required to achieve similar sensitivity. Two different commercial multiple reaction monitoring kits and an antibody-based multiplexing kit were used to compare the apolipoprotein measurements in a subset of samples. In general, good agreement was observed between the 2 multiple reaction monitoring kits, but some of the multiple reaction monitoring–based measurements differed from antibody-based assays. Conclusions—The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.

Original language	English
Journal	Circulation-Cardiovascular Genetics
Volume	10
Issue number	6
Early online date	13 Dec 2017
DOIs	https://doi.org/10.1161/CIRCGENETICS.117.001808
Publication status	Published - Dec 2017

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Yin, X., Baig, F., Haudebourg, E., Blankley, R. T., Gandhi, T., Müller, S., Reiter, L., Hinterwirth, H., Pechlaner, R., Tsimikas, S., Santer, P., Willeit, J., Kiechl, S., Witztum, J. L., Sullivan, A., & Mayr, M. (2017). Plasma Proteomics for Epidemiology: Increasing Throughput with Standard-Flow Rates. Circulation-Cardiovascular Genetics, 10(6). https://doi.org/10.1161/CIRCGENETICS.117.001808

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title = "Plasma Proteomics for Epidemiology: Increasing Throughput with Standard-Flow Rates",

abstract = "Background—Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. Methods and Results—Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS (<0.05 minutes) compared with the nanoflow LC-MS method (0.26–0.44 minutes). In addition, the standard-flow LC method also offered less variation in protein measurements. However, 5× more sample volume was required to achieve similar sensitivity. Two different commercial multiple reaction monitoring kits and an antibody-based multiplexing kit were used to compare the apolipoprotein measurements in a subset of samples. In general, good agreement was observed between the 2 multiple reaction monitoring kits, but some of the multiple reaction monitoring–based measurements differed from antibody-based assays. Conclusions—The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.",

author = "Xiaoke Yin and Ferheen Baig and Eloi Haudebourg and Blankley, {Richard T.} and Tejas Gandhi and Sebastian M{\"u}ller and Lukas Reiter and Helmut Hinterwirth and Raimund Pechlaner and Sotirios Tsimikas and Peter Santer and Johann Willeit and Stefan Kiechl and Witztum, {Joseph L.} and Anthony Sullivan and Manuel Mayr",

year = "2017",

month = dec,

doi = "10.1161/CIRCGENETICS.117.001808",

language = "English",

volume = "10",

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Yin, X , Baig, F , Haudebourg, E, Blankley, RT, Gandhi, T, Müller, S, Reiter, L, Hinterwirth, H, Pechlaner, R, Tsimikas, S, Santer, P, Willeit, J, Kiechl, S, Witztum, JL, Sullivan, A & Mayr, M 2017, 'Plasma Proteomics for Epidemiology: Increasing Throughput with Standard-Flow Rates', Circulation-Cardiovascular Genetics, vol. 10, no. 6. https://doi.org/10.1161/CIRCGENETICS.117.001808

TY - JOUR

T1 - Plasma Proteomics for Epidemiology

T2 - Increasing Throughput with Standard-Flow Rates

AU - Yin, Xiaoke

AU - Baig, Ferheen

AU - Haudebourg, Eloi

AU - Blankley, Richard T.

AU - Gandhi, Tejas

AU - Müller, Sebastian

AU - Reiter, Lukas

AU - Hinterwirth, Helmut

AU - Pechlaner, Raimund

AU - Tsimikas, Sotirios

AU - Santer, Peter

AU - Willeit, Johann

AU - Kiechl, Stefan

AU - Witztum, Joseph L.

AU - Sullivan, Anthony

AU - Mayr, Manuel

PY - 2017/12

Y1 - 2017/12

N2 - Background—Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. Methods and Results—Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS (<0.05 minutes) compared with the nanoflow LC-MS method (0.26–0.44 minutes). In addition, the standard-flow LC method also offered less variation in protein measurements. However, 5× more sample volume was required to achieve similar sensitivity. Two different commercial multiple reaction monitoring kits and an antibody-based multiplexing kit were used to compare the apolipoprotein measurements in a subset of samples. In general, good agreement was observed between the 2 multiple reaction monitoring kits, but some of the multiple reaction monitoring–based measurements differed from antibody-based assays. Conclusions—The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.

AB - Background—Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. Methods and Results—Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS (<0.05 minutes) compared with the nanoflow LC-MS method (0.26–0.44 minutes). In addition, the standard-flow LC method also offered less variation in protein measurements. However, 5× more sample volume was required to achieve similar sensitivity. Two different commercial multiple reaction monitoring kits and an antibody-based multiplexing kit were used to compare the apolipoprotein measurements in a subset of samples. In general, good agreement was observed between the 2 multiple reaction monitoring kits, but some of the multiple reaction monitoring–based measurements differed from antibody-based assays. Conclusions—The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.

U2 - 10.1161/CIRCGENETICS.117.001808

DO - 10.1161/CIRCGENETICS.117.001808

M3 - Article

SN - 1942-325X

VL - 10

JO - Circulation-Cardiovascular Genetics

JF - Circulation-Cardiovascular Genetics

IS - 6

ER -

Plasma Proteomics for Epidemiology: Increasing Throughput with Standard-Flow Rates

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