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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

Impact of Sample Preparation Strategies on The Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics

Project description:Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clinical studies are based on the differential expression of certain proteins that can be used as biomarkers or be indicative for a pathological state. In this study, we performed a direct comparison of 6 widely used serum proteomic sample preparation workflows: In-gel digestion (IGD), Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), Top 14 Abundant Protein Depletion (Top 14), Isopropanol/Trichloroacetic Acid (IPA/TCA) precipitation, PreOmics ENRICH-iST (PreOmics), and Seer Proteograph XT (Seer). Seer and PreOmics demonstrated superior quantitative accuracy especially for proteins with low abundance in serum while Seer enrichment approach provided the highest number of protein identifications (> 2000) as measured by an Orbitrap Exploris 480. All methods had median CVs close to or below 20%. This comparative analysis provides a comprehensive resource for selecting the most appropriate serum sample preparation strategy based on specific experimental needs, facilitating human serum proteomic profiling for biomedical research.

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Human Bone Marrow Interstitial Fluid Plasma Cell Dyscrasias LC-MSMS

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Comparison of deep plasma proteome enrichment methods

Project description:Plasma is a complex biological fluid containing extracellular vesicles (EVs), residual platelets, and soluble proteins, all of which can serve as biomarkers for pathological conditions. While conventional plasma proteomics typically identifies hundreds of proteins, recent enrichment strategies have expanded coverage to thousands. It is not clear yet whether these methods enrich preferentially different classes of protein and whether they allow for reliable quantification Here, we compared three common advanced proteomic workflows—Seer Proteograph (nanoparticle-based), MagNET (SCX magnetic beads), and ENRICHplus (PreOmics)—as well as EV enrichment obtained by centrifugation. We aimed to explore the content in soluble proteins, EV cargo, and platelet-derived proteins in platelet-poor plasma (PPP) from healthy donors after the enrichments. Samples were analyzed using timsTOF platforms and quantified with DIA-NN in library-free mode. Functional insights were obtained using Over-Representation Analysis (ORA), Human Protein Atlas annotations, and EV-specific markers. Quantification was evaluated comparing each method to neat plasma using protein coefficient of variation and point-biserial correlation. We quantified an average of ~4500 proteins with EV centrifugation, ~4000 with Seer, ~2800 with ENRICHplus, ~2300 with MagNET, and ~900 with neat plasma. Each method enriched distinct protein signatures: EV markers such as CD81 were predominantly detected in EV preparations; lipoproteins were enriched in ENRICHplus; cytokine and hormone signaling pathways were most evident in Seer. Platelet protein intensity was directly correlated with total protein identifications but did not compromise quantification of low-abundance proteins. Across 50 healthy individuals, Proteograph consistently demonstrated reproducible enrichment and depletion patterns, with notable exceptions for proteins such as FCN3, F11, and FCGBP.

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2025-02-17 | PXD053704 | panorama

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