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A Technical Evaluation of Plasma Proteomics Technologies

ABSTRACT: We report a technical evaluation of six notable plasma proteomics technologies from recent years. Unenriched plasma, perchloric acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph XT, and Olink Explore HT. The methods were compared on proteomic depth, reproducibility, linearity, tolerance to lipid interference, and limit of detection/quantification. We also tested the applicability of these methods for detecting differences between healthy and cancer groups in a non-small cell lung cancer cohort.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Joshua Coon

LAB HEAD: Dr Joshua Coon

PROVIDER: PAD000002 | Pride | 2025-05-12

REPOSITORIES: Pride

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	P2024-198-OLI_HT_93_2024-10-10_npx.parquet	Other
	P2024-198-OLI_HT_93_Analysis_Report_2024-10-10.pdf	Pdf
	PRIDE_Upload_FileInformation_Olink.xlsx	Xlsx
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Publications

Technical Evaluation of Plasma Proteomics Technologies.

Beimers William F WF Overmyer Katherine A KA Sinitcyn Pavel P Lancaster Noah M NM Quarmby Scott T ST Coon Joshua J JJ

Journal of proteome research 20250514 6

Plasma proteomics technologies are rapidly evolving and of critical importance to the field of biomedical research. Here, we report a technical evaluation of six notable plasma proteomics technologies─unenriched (Neat), acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph XT, and Olink Explore HT. The methods were compared on proteomic depth, reproducibility, linearity, tolerance to lipid interference, and limit of detection/quantification. In total, we performed 618 LC-MS/MS experimen ...[more]

PMID: 40366296

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A Technical Evaluation of Plasma Proteomics Technologies

Project description:We report a technical evaluation of six notable plasma proteomics technologies from recent years. Unenriched plasma, perchloric acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph XT, and Olink Explore HT. The methods were compared on proteomic depth, reproducibility, linearity, tolerance to lipid interference, and limit of detection/quantification. We also tested the applicability of these methods for detecting differences between healthy and cancer groups in a non-small cell lung cancer cohort.

2025-05-12 | PXD060573 | Pride

Evaluation of Olink Reveal Proximity Extension Assay for High-Throughput Proteomics: A Case Study Using NIST SRM 1950 and Spike-In Protein Standards

Project description:Plasma proteomics has regained attention in recent years through advancements in mass spectrometry instrumentation and sample preparation, as well as new high-throughput affinity-based technologies. Here, we evaluate the analytical performance of the new Olink Reveal platform, a proximity extension assay based technology quantifying 1,034 proteins across biological pathways. Using spiked-in recombinant Interleukin-10 (IL-10) and vascular endothelial growth factor D (VEGF-D) in the NIST SRM 1950 plasma standard, we assessed the linearity, sensitivity, precision and accuracy of the Olink assay. The results demonstrated strong linear relationships (R² 0.922–0.953) for both IL-10 and VEGF-D across spiked-in concentrations, confirming the robust technical performance of Olink Reveal and underscoring its suitability for relative quantitation in large-scale studies. The resulting data contains no sensitive or personally identifiable information, and is available in public repositories, and therefore suitable for use in benchmarking and software development.

2025-06-03 | PAD000009 | Pride

TIMEPOINT, a phase 1 study of MTL-CEBPA in combination with pembrolizumab, supports the immunomodulatory effect of MTL-CEBPA in solid tumours.

Project description:Many cancer patients don’t benefit from currently-approved immune checkpoint inhibitors (ICI), suggesting that additional immunomodulation of the immunosuppressive tumour microenvironment (TME) is required. MTL-CEBPA specifically upregulates expression of master myeloid transcription factor, CEBPA, relieving myeloid-driven immunosuppression. Here, we report the safety, tolerability, pharmacokinetics, and efficacy of MTL-CEBPA in combination with pembrolizumab in patients with advanced solid tumours that typically show ICI resistance. Multimodal exploratory analyses of paired patient biopsies demonstrate biological changes associated with combination treatment of MTL-CEBPA and pembrolizumab, including increased infiltration of T cell and antigen-presenting cells supporting conversion from an immune desert towards a more immune-inflamed TME. Patients with disease stabilisation demonstrate reductions in immunosuppressive myeloid cells post-treatment. Collectively, these data support a role for MTL-CEBPA in reducing immunosuppression in the TME. This study was registered at ClinicalTrials.gov (NCT04105335). This manuscript also reports proteomic data from patients treated with MTL-CEBPA in combination with sorafenib from clinical trial, OUTREACH, accessible at ClinicalTrials.gov, number NCT02716012 and reported. Stored plasma from patients from this clinical trial were analysed using OLINK as described below.

2025-05-07 | PXD060726 | Pride

Overexpression of Let-7a Mitigates Diploidization in Mouse Androgenetic Haploid Embryonic Stem Cells

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2025-01-24 | PXD059624 | Pride

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2022-08-12 | PXD031628 | Pride

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