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Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma

[Image: see text] Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few ca...

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Autores principales: Kennedy, Jacob J., Whiteaker, Jeffrey R., Ivey, Richard G., Burian, Aura, Chowdhury, Shrabanti, Tsai, Chia-Feng, Liu, Tao, Lin, ChenWei, Murillo, Oscar D., Lundeen, Rachel A., Jones, Lisa A., Gafken, Philip R., Longton, Gary, Rodland, Karin D., Skates, Steven J., Landua, John, Wang, Pei, Lewis, Michael T., Paulovich, Amanda G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9280723/
https://www.ncbi.nlm.nih.gov/pubmed/35767427
http://dx.doi.org/10.1021/acs.analchem.1c04382
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author Kennedy, Jacob J.
Whiteaker, Jeffrey R.
Ivey, Richard G.
Burian, Aura
Chowdhury, Shrabanti
Tsai, Chia-Feng
Liu, Tao
Lin, ChenWei
Murillo, Oscar D.
Lundeen, Rachel A.
Jones, Lisa A.
Gafken, Philip R.
Longton, Gary
Rodland, Karin D.
Skates, Steven J.
Landua, John
Wang, Pei
Lewis, Michael T.
Paulovich, Amanda G.
author_facet Kennedy, Jacob J.
Whiteaker, Jeffrey R.
Ivey, Richard G.
Burian, Aura
Chowdhury, Shrabanti
Tsai, Chia-Feng
Liu, Tao
Lin, ChenWei
Murillo, Oscar D.
Lundeen, Rachel A.
Jones, Lisa A.
Gafken, Philip R.
Longton, Gary
Rodland, Karin D.
Skates, Steven J.
Landua, John
Wang, Pei
Lewis, Michael T.
Paulovich, Amanda G.
author_sort Kennedy, Jacob J.
collection PubMed
description [Image: see text] Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R(2) > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.
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spelling pubmed-92807232022-07-15 Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma Kennedy, Jacob J. Whiteaker, Jeffrey R. Ivey, Richard G. Burian, Aura Chowdhury, Shrabanti Tsai, Chia-Feng Liu, Tao Lin, ChenWei Murillo, Oscar D. Lundeen, Rachel A. Jones, Lisa A. Gafken, Philip R. Longton, Gary Rodland, Karin D. Skates, Steven J. Landua, John Wang, Pei Lewis, Michael T. Paulovich, Amanda G. Anal Chem [Image: see text] Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R(2) > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers. American Chemical Society 2022-06-29 2022-07-12 /pmc/articles/PMC9280723/ /pubmed/35767427 http://dx.doi.org/10.1021/acs.analchem.1c04382 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Kennedy, Jacob J.
Whiteaker, Jeffrey R.
Ivey, Richard G.
Burian, Aura
Chowdhury, Shrabanti
Tsai, Chia-Feng
Liu, Tao
Lin, ChenWei
Murillo, Oscar D.
Lundeen, Rachel A.
Jones, Lisa A.
Gafken, Philip R.
Longton, Gary
Rodland, Karin D.
Skates, Steven J.
Landua, John
Wang, Pei
Lewis, Michael T.
Paulovich, Amanda G.
Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
title Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
title_full Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
title_fullStr Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
title_full_unstemmed Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
title_short Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
title_sort internal standard triggered-parallel reaction monitoring mass spectrometry enables multiplexed quantification of candidate biomarkers in plasma
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9280723/
https://www.ncbi.nlm.nih.gov/pubmed/35767427
http://dx.doi.org/10.1021/acs.analchem.1c04382
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