ASMS 2026: Streamlined Plasma Proteomics Reveals Condition-Specific Apolipoprotein E and Fibrinogen Dynamics
Top-3 LFQ with automated %RSD filtering surfaces condition-specific isoform biology from Seer Proteograph XT-enriched plasma
About this Poster
Plasma proteomics is famously hard — high dynamic range, dominant abundant proteins, isoform overlap. This poster applies Protein Metrics' Multi-Protein Quantitation workflow to Seer Proteograph XT-enriched plasma (~4,500 proteins detected) to show how automated %RSD filtering, replicate-based identification thresholds, and Top-3 unique-peptide LFQ make condition-specific biology jump out of the data without manual hand-holding. The result: consistent ApoE upregulation in NPA fractions and fibrinogen isoform elevation in NPB, confirmed across multiple peptides and replicates and surfaced by the workflow's interactive visualizations.
Key Learnings:
- See how stacked-XIC bar charts reveal condition-specific differential expression at a glance across NPA and NPB replicate sets.
- Understand how automated %RSD filtering and replicate-based thresholds enforce reproducibility without manual review of every protein.
- Learn how Top-3 unique-peptide LFQ resolves isoform-level biology — ApoE in NPA; fibrinogen α/β/γ in NPB — that peptide-shared methods can collapse.
- Compare the Multi-Protein Quantitation workflow to the corresponding Multi-Protein Quan-DIA workflow for deeper coverage and stronger reproducibility on low-abundance peptides.
Public dataset from Beimers et al. (J. Proteome Res. 2025; PRIDE PXD060573). Thanks to Lucas Calestini (Real Retina Analytics) for analytical advice.