Head-to-Head Comparison of Aptamer- and Antibody-Based Proteomic Platforms in Human Cerebrospinal Fluid Samples from a Real-World Memory Clinic Cohort

Raquel Puerta; Amanda Cano; Pablo García-González; Fernando García-Gutiérrez; Maria Capdevila; Itziar de Rojas; Clàudia Olivé; Josep Blázquez-Folch; Oscar Sotolongo-Grau; Andrea Miguel; Laura Montrreal; Pamela Martino-Adami; Asif Khan; Adelina Orellana; Yun Ju Sung; Ruth Frikke-Schmidt; Natalie Marchant; Jean Charles Lambert; Maitée Rosende-Roca; Montserrat Alegret; Maria Victoria Fernández; Marta Marquié; Sergi Valero; Lluís Tárraga; Carlos Cruchaga; Alfredo Ramírez; Mercè Boada; Bart Smets; Alfredo Cabrera-Socorro; Agustín Ruiz

doi:10.3390/ijms26010286

Head-to-Head Comparison of Aptamer- and Antibody-Based Proteomic Platforms in Human Cerebrospinal Fluid Samples from a Real-World Memory Clinic Cohort

Raquel Puerta, Amanda Cano, Pablo García-González, Fernando García-Gutiérrez, Maria Capdevila, Itziar de Rojas, Clàudia Olivé, Josep Blázquez-Folch, Oscar Sotolongo-Grau, Andrea Miguel, Laura Montrreal, Pamela Martino-Adami, Asif Khan, Adelina Orellana, Yun Ju Sung, Ruth Frikke-Schmidt, Natalie Marchant, Jean Charles Lambert, Maitée Rosende-Roca, Montserrat AlegretMaria Victoria Fernández, Marta Marquié, Sergi Valero, Lluís Tárraga, Carlos Cruchaga, Alfredo Ramírez, Mercè Boada, Bart Smets, Alfredo Cabrera-Socorro, Agustín Ruiz^*

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Abstract

High-throughput proteomic platforms are crucial to identify novel Alzheimer’s disease (AD) biomarkers and pathways. In this study, we evaluated the reproducibility and reliability of aptamer-based (SomaScan^® 7k) and antibody-based (Olink^® Explore 3k) proteomic platforms in cerebrospinal fluid (CSF) samples from the Ace Alzheimer Center Barcelona real-world cohort. Intra- and inter-platform reproducibility were evaluated through correlations between two independent SomaScan^® assays analyzing the same samples, and between SomaScan^® and Olink^® results. Association analyses were performed between proteomic measures, CSF biological traits, sample demographics, and AD endophenotypes. Our 12-category metric of reproducibility combining correlation analyses identified 2428 highly reproducible SomaScan CSF measures, with over 600 proteins well reproduced on another proteomic platform. The association analyses among AD clinical phenotypes revealed that the significant associations mainly involved reproducible proteins. The validation of reproducibility in these novel proteomics platforms, measured using this scarce biomaterial, is essential for accurate analysis and proper interpretation of innovative results. This classification metric could enhance confidence in multiplexed proteomic platforms and improve the design of future panels.

Originalsprog	Engelsk
Artikelnummer	286
Tidsskrift	International Journal of Molecular Sciences
Vol/bind	26
Udgave nummer	1
Antal sider	23
ISSN	1661-6596
DOI	https://doi.org/10.3390/ijms26010286
Status	Udgivet - 2025

Bibliografisk note

Publisher Copyright:
© 2024 by the authors.

Adgang til dokumentet

10.3390/ijms26010286Licens: CC BY

FulltextForlagets udgivne version, 2,42 MBLicens: CC BY

Citationsformater

Puerta, R., Cano, A., García-González, P., García-Gutiérrez, F., Capdevila, M., de Rojas, I., Olivé, C., Blázquez-Folch, J., Sotolongo-Grau, O., Miguel, A., Montrreal, L., Martino-Adami, P., Khan, A., Orellana, A., Sung, Y. J., Frikke-Schmidt, R., Marchant, N., Lambert, J. C., Rosende-Roca, M., ... Ruiz, A. (2025). Head-to-Head Comparison of Aptamer- and Antibody-Based Proteomic Platforms in Human Cerebrospinal Fluid Samples from a Real-World Memory Clinic Cohort. International Journal of Molecular Sciences, 26(1), Artikel 286. https://doi.org/10.3390/ijms26010286

Head-to-Head Comparison of Aptamer- and Antibody-Based Proteomic Platforms in Human Cerebrospinal Fluid Samples from a Real-World Memory Clinic Cohort. / Puerta, Raquel; Cano, Amanda; García-González, Pablo et al.
I: International Journal of Molecular Sciences, Bind 26, Nr. 1, 286, 2025.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Puerta, R, Cano, A, García-González, P, García-Gutiérrez, F, Capdevila, M, de Rojas, I, Olivé, C, Blázquez-Folch, J, Sotolongo-Grau, O, Miguel, A, Montrreal, L, Martino-Adami, P, Khan, A, Orellana, A, Sung, YJ, Frikke-Schmidt, R, Marchant, N, Lambert, JC, Rosende-Roca, M, Alegret, M, Fernández, MV, Marquié, M, Valero, S, Tárraga, L, Cruchaga, C, Ramírez, A, Boada, M, Smets, B, Cabrera-Socorro, A & Ruiz, A 2025, 'Head-to-Head Comparison of Aptamer- and Antibody-Based Proteomic Platforms in Human Cerebrospinal Fluid Samples from a Real-World Memory Clinic Cohort', International Journal of Molecular Sciences, bind 26, nr. 1, 286. https://doi.org/10.3390/ijms26010286

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abstract = "High-throughput proteomic platforms are crucial to identify novel Alzheimer{\textquoteright}s disease (AD) biomarkers and pathways. In this study, we evaluated the reproducibility and reliability of aptamer-based (SomaScan{\textregistered} 7k) and antibody-based (Olink{\textregistered} Explore 3k) proteomic platforms in cerebrospinal fluid (CSF) samples from the Ace Alzheimer Center Barcelona real-world cohort. Intra- and inter-platform reproducibility were evaluated through correlations between two independent SomaScan{\textregistered} assays analyzing the same samples, and between SomaScan{\textregistered} and Olink{\textregistered} results. Association analyses were performed between proteomic measures, CSF biological traits, sample demographics, and AD endophenotypes. Our 12-category metric of reproducibility combining correlation analyses identified 2428 highly reproducible SomaScan CSF measures, with over 600 proteins well reproduced on another proteomic platform. The association analyses among AD clinical phenotypes revealed that the significant associations mainly involved reproducible proteins. The validation of reproducibility in these novel proteomics platforms, measured using this scarce biomaterial, is essential for accurate analysis and proper interpretation of innovative results. This classification metric could enhance confidence in multiplexed proteomic platforms and improve the design of future panels.",

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author = "Raquel Puerta and Amanda Cano and Pablo Garc{\'i}a-Gonz{\'a}lez and Fernando Garc{\'i}a-Guti{\'e}rrez and Maria Capdevila and {de Rojas}, Itziar and Cl{\`a}udia Oliv{\'e} and Josep Bl{\'a}zquez-Folch and Oscar Sotolongo-Grau and Andrea Miguel and Laura Montrreal and Pamela Martino-Adami and Asif Khan and Adelina Orellana and Sung, {Yun Ju} and Ruth Frikke-Schmidt and Natalie Marchant and Lambert, {Jean Charles} and Mait{\'e}e Rosende-Roca and Montserrat Alegret and Fern{\'a}ndez, {Maria Victoria} and Marta Marqui{\'e} and Sergi Valero and Llu{\'i}s T{\'a}rraga and Carlos Cruchaga and Alfredo Ram{\'i}rez and Merc{\`e} Boada and Bart Smets and Alfredo Cabrera-Socorro and Agust{\'i}n Ruiz",

note = "Publisher Copyright: {\textcopyright} 2024 by the authors.",

year = "2025",

doi = "10.3390/ijms26010286",

language = "English",

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journal = "International Journal of Molecular Sciences",

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T1 - Head-to-Head Comparison of Aptamer- and Antibody-Based Proteomic Platforms in Human Cerebrospinal Fluid Samples from a Real-World Memory Clinic Cohort

AU - Puerta, Raquel

AU - Cano, Amanda

AU - García-González, Pablo

AU - García-Gutiérrez, Fernando

AU - Capdevila, Maria

AU - de Rojas, Itziar

AU - Olivé, Clàudia

AU - Blázquez-Folch, Josep

AU - Sotolongo-Grau, Oscar

AU - Miguel, Andrea

AU - Montrreal, Laura

AU - Martino-Adami, Pamela

AU - Khan, Asif

AU - Orellana, Adelina

AU - Sung, Yun Ju

AU - Frikke-Schmidt, Ruth

AU - Marchant, Natalie

AU - Lambert, Jean Charles

AU - Rosende-Roca, Maitée

AU - Alegret, Montserrat

AU - Fernández, Maria Victoria

AU - Marquié, Marta

AU - Valero, Sergi

AU - Tárraga, Lluís

AU - Cruchaga, Carlos

AU - Ramírez, Alfredo

AU - Boada, Mercè

AU - Smets, Bart

AU - Cabrera-Socorro, Alfredo

AU - Ruiz, Agustín

PY - 2025

Y1 - 2025

N2 - High-throughput proteomic platforms are crucial to identify novel Alzheimer’s disease (AD) biomarkers and pathways. In this study, we evaluated the reproducibility and reliability of aptamer-based (SomaScan® 7k) and antibody-based (Olink® Explore 3k) proteomic platforms in cerebrospinal fluid (CSF) samples from the Ace Alzheimer Center Barcelona real-world cohort. Intra- and inter-platform reproducibility were evaluated through correlations between two independent SomaScan® assays analyzing the same samples, and between SomaScan® and Olink® results. Association analyses were performed between proteomic measures, CSF biological traits, sample demographics, and AD endophenotypes. Our 12-category metric of reproducibility combining correlation analyses identified 2428 highly reproducible SomaScan CSF measures, with over 600 proteins well reproduced on another proteomic platform. The association analyses among AD clinical phenotypes revealed that the significant associations mainly involved reproducible proteins. The validation of reproducibility in these novel proteomics platforms, measured using this scarce biomaterial, is essential for accurate analysis and proper interpretation of innovative results. This classification metric could enhance confidence in multiplexed proteomic platforms and improve the design of future panels.

AB - High-throughput proteomic platforms are crucial to identify novel Alzheimer’s disease (AD) biomarkers and pathways. In this study, we evaluated the reproducibility and reliability of aptamer-based (SomaScan® 7k) and antibody-based (Olink® Explore 3k) proteomic platforms in cerebrospinal fluid (CSF) samples from the Ace Alzheimer Center Barcelona real-world cohort. Intra- and inter-platform reproducibility were evaluated through correlations between two independent SomaScan® assays analyzing the same samples, and between SomaScan® and Olink® results. Association analyses were performed between proteomic measures, CSF biological traits, sample demographics, and AD endophenotypes. Our 12-category metric of reproducibility combining correlation analyses identified 2428 highly reproducible SomaScan CSF measures, with over 600 proteins well reproduced on another proteomic platform. The association analyses among AD clinical phenotypes revealed that the significant associations mainly involved reproducible proteins. The validation of reproducibility in these novel proteomics platforms, measured using this scarce biomaterial, is essential for accurate analysis and proper interpretation of innovative results. This classification metric could enhance confidence in multiplexed proteomic platforms and improve the design of future panels.

KW - Alzheimer’s disease

KW - biomarkers

KW - cerebrospinal fluid

KW - mild cognitive impairment

KW - Olink

KW - proteomics

KW - SomaScan

U2 - 10.3390/ijms26010286

DO - 10.3390/ijms26010286

M3 - Journal article

C2 - 39796148

AN - SCOPUS:85214508578

SN - 1661-6596

VL - 26

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

IS - 1

M1 - 286

ER -