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Optimised plasma sample preparation and LC‐MS analysis to support large‐scale proteomic analysis of clinical trial specimens: Application to the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial

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dc.contributor.author O’Rourke, Matthew B. en_US
dc.contributor.author GALANDE, SANJEEV et al. en_US
dc.date.accessioned 2023-03-31T09:43:49Z
dc.date.available 2023-03-31T09:43:49Z
dc.date.issued 2023-05 en_US
dc.identifier.citation Proteomics - Clinical Applications, 17(03). en_US
dc.identifier.issn 1862-8346 en_US
dc.identifier.issn 1862-8354 en_US
dc.identifier.uri https://doi.org/10.1002/prca.202200106 en_US
dc.identifier.uri http://dr.iiserpune.ac.in:8080/xmlui/handle/123456789/7682
dc.description.abstract Purpose Robust, affordable plasma proteomic biomarker workflows are needed for large-scale clinical studies. We evaluated aspects of sample preparation to allow liquid chromatography-mass spectrometry (LC-MS) analysis of more than 1500 samples from the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial of adults with type 2 diabetes. Methods Using LC-MS with data-independent acquisition we evaluated four variables: plasma protein depletion, EDTA or citrated anti-coagulant blood collection tubes, plasma lipid depletion strategies and plasma freeze–thaw cycles. Optimised methods were applied in a pilot study of FIELD participants. Results LC-MS of undepleted plasma conducted over a 45 min gradient yielded 172 proteins after excluding immunoglobulin isoforms. Cibachrome-blue-based depletion yielded additional proteins but with cost and time expenses, while immunodepleting albumin and IgG provided few additional identifications. Only minor variations were associated with blood collection tube type, delipidation methods and freeze–thaw cycles. From 65 batches involving over 1500 injections, the median intra-batch quantitative differences in the top 100 proteins of the plasma external standard were less than 2%. Fenofibrate altered seven plasma proteins. Conclusions and clinical relevance A robust plasma handling and LC-MS proteomics workflow for abundant plasma proteins has been developed for large-scale biomarker studies that balance proteomic depth with time and resource costs. en_US
dc.language.iso en en_US
dc.publisher Wiley en_US
dc.subject Plasma en_US
dc.subject Mass spectrometry en_US
dc.subject Proteomics en_US
dc.subject Biomarker en_US
dc.subject Diabetes en_US
dc.subject Fenofibrate en_US
dc.subject 2023-MAR-WEEK4 en_US
dc.subject TOC-MAR-2023 en_US
dc.subject 2023 en_US
dc.title Optimised plasma sample preparation and LC‐MS analysis to support large‐scale proteomic analysis of clinical trial specimens: Application to the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial en_US
dc.type Article en_US
dc.contributor.department Dept. of Biology en_US
dc.identifier.sourcetitle Proteomics - Clinical Applications en_US
dc.publication.originofpublisher Foreign en_US


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