Systematic evaluation of analytical methods for CSF proteomics

TL;DR

This study compares different methods for analyzing proteins in cerebrospinal fluid to determine which is best suited for various research goals.

Contribution

The paper provides a systematic benchmark of five CSF proteomics workflows, revealing their strengths and limitations for translational neuro-oncology.

Findings

Seer achieved the highest proteomic depth with ~17,000 unique peptides detected.

Each workflow highlighted distinct biological signatures, such as mitochondrial, lysosomal, or nuclear proteins.

The study found no single method is universally optimal; workflow choice should align with research goals and constraints.

Abstract

Cerebrospinal fluid (CSF) provides a unique window into brain pathology, yet challenges in unbiased mass-spectrometric (MS) discovery persist due to sample complexity and the need for optimized analytical workflows. Multiple laboratory workflows have been developed for CSF proteomics, each with distinct advantages for specific applications. To interrogate which laboratory workflow is most suitable for this biological matrix, we benchmarked five orthogonal sample-preparation strategies—MStern, Proteograph™ nanoparticle enrichment (Seer), N-glycopeptide capture (N-Gp), and two extracellular-vesicle (EV) fractions isolated by differential ultracentrifugation (P20- and P150-EV)—in CSF from 19 patients with central nervous system lymphoma. The protocols span a practical spectrum of input volume (6000–50 μL), hands-on time, and reagent cost, enabling informed method selection for translational applications. In total we performed 82 LC-MS/MS experiments and detected over 38,000 unique peptides and more than 3000 proteins across all modalities. Seer achieved the best proteomic depth (~ 17,000 unique peptides) and the tightest detection across samples, followed by P20-EV (~ 9,000), MStern (~ 5,500), P150-EV (~ 5,000), and N-Gp (~ 1,000). None of the methods introduced systematic bias in peptide or protein isoelectric point or hydrophobicity, yet each selectively highlighted distinct biological niches: P20-EVs favoured mitochondrial signatures, N-Gp capture lysosomal and plasma membrane signatures and Seer enhanced nuclear representation. These findings demonstrate that no single protocol suffices for every research question; instead, workflow selection should align with sample-volume constraints, budget and biological question. Our comparative framework empowers investigators to match CSF proteomics strategies to specific neuro-oncological objectives, thereby accelerating the translation of CSF biomarkers into clinically actionable assays.

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