An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma
Blood plasma is one of the most widely used samples for cancer biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-a...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-09-01
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| Series: | Frontiers in Oncology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fonc.2020.543997/full |
| _version_ | 1818523038693457920 |
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| author | Vipin Kumar Sandipan Ray Saicharan Ghantasala Sanjeeva Srivastava |
| author_facet | Vipin Kumar Sandipan Ray Saicharan Ghantasala Sanjeeva Srivastava |
| author_sort | Vipin Kumar |
| collection | DOAJ |
| description | Blood plasma is one of the most widely used samples for cancer biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-abundance proteins. Here we have described an optimized, integrated quantitative proteomics pipeline combining the label-free and multiplexed-labeling-based (iTRAQ and TMT) plasma proteome profiling methods for biomarker discovery, followed by the targeted approaches for validation of the identified potential marker proteins. In this workflow, the targeted quantitation of proteins is carried out by multiple-reaction monitoring (MRM) and parallel-reaction monitoring (PRM) mass spectrometry. Thus, our approach enables both unbiased screenings of biomarkers and their subsequent selective validation in human plasma. The overall procedure takes only ~2 days to complete, including the time for data acquisition (excluding database searching). This protocol is quick, flexible, and eliminates the need for a separate immunoassay-based validation workflow in blood cancer biomarker investigations. We anticipate that this plasma proteomics workflow will help to accelerate the cancer biomarker discovery program and provide a valuable resource to the cancer research community. |
| first_indexed | 2024-12-11T05:40:23Z |
| format | Article |
| id | doaj.art-207a2ad5949c4665ae79ac328dc9d0b4 |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-12-11T05:40:23Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-207a2ad5949c4665ae79ac328dc9d0b42022-12-22T01:19:08ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2020-09-011010.3389/fonc.2020.543997543997An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in PlasmaVipin KumarSandipan RaySaicharan GhantasalaSanjeeva SrivastavaBlood plasma is one of the most widely used samples for cancer biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-abundance proteins. Here we have described an optimized, integrated quantitative proteomics pipeline combining the label-free and multiplexed-labeling-based (iTRAQ and TMT) plasma proteome profiling methods for biomarker discovery, followed by the targeted approaches for validation of the identified potential marker proteins. In this workflow, the targeted quantitation of proteins is carried out by multiple-reaction monitoring (MRM) and parallel-reaction monitoring (PRM) mass spectrometry. Thus, our approach enables both unbiased screenings of biomarkers and their subsequent selective validation in human plasma. The overall procedure takes only ~2 days to complete, including the time for data acquisition (excluding database searching). This protocol is quick, flexible, and eliminates the need for a separate immunoassay-based validation workflow in blood cancer biomarker investigations. We anticipate that this plasma proteomics workflow will help to accelerate the cancer biomarker discovery program and provide a valuable resource to the cancer research community.https://www.frontiersin.org/article/10.3389/fonc.2020.543997/fullcancer biomarkermultiplexed quantitative proteomicstargeted proteomicslabel-free quantitationmultiple reaction monitoringparallel reaction monitoring |
| spellingShingle | Vipin Kumar Sandipan Ray Saicharan Ghantasala Sanjeeva Srivastava An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma Frontiers in Oncology cancer biomarker multiplexed quantitative proteomics targeted proteomics label-free quantitation multiple reaction monitoring parallel reaction monitoring |
| title | An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma |
| title_full | An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma |
| title_fullStr | An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma |
| title_full_unstemmed | An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma |
| title_short | An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma |
| title_sort | integrated quantitative proteomics workflow for cancer biomarker discovery and validation in plasma |
| topic | cancer biomarker multiplexed quantitative proteomics targeted proteomics label-free quantitation multiple reaction monitoring parallel reaction monitoring |
| url | https://www.frontiersin.org/article/10.3389/fonc.2020.543997/full |
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