Blood/Plasma/Serum Proteomics Solutions

Undepleted vs Depleted Plasma Proteomics: How to Choose

Most labs default to depletion because that's what they've always done. The right choice depends on what you're actually trying to measure and how many samples you have.

Still not sure which path fits your project? The practical answer is often:

This two-tier approach gives you both statistical power and mechanistic depth — at roughly half the cost of running the entire cohort through depletion.

What Undepleted Plasma DIA Detects

The question we hear most often: "If I don't deplete, am I just measuring albumin and a few acute phase proteins?" The answer is no — and the data proves it.

In undepleted plasma DIA, albumin and IgG still dominate the total ion current, but DIA's systematic fragmentation captures peptides from proteins across the full dynamic range. The 1,000+ proteins you identify are distributed across all major plasma protein classes:

What you won't see without depletion: most interleukins, TNF-family cytokines, chemokines below ~100 pg/mL, and very low-abundance tissue-specific proteins. These require the deep workflow — or, for the lowest-abundance targets, affinity-based methods. Our service is transparent about these boundaries because choosing the right tool matters more than claiming universal coverage.

Same undepleted plasma sample, two acquisition methods. DDA: 380 proteins. DIA: 1,220 proteins. The difference is systematic precursor fragmentation — not a different sample or protocol.

Protein classes quantified from undepleted plasma — complement, coagulation, apolipoproteins, protease inhibitors, and tissue leakage markers all represented across abundance tiers.

CV distribution across a 500-sample undepleted plasma cohort. Median CV below 15% — the simpler prep translates directly to better reproducibility at scale.

Deep Plasma Proteomics with Depletion and Fractionation

Some biological questions live entirely in the low-abundance range. Cytokine storm characterization. Growth factor signaling in tumor microenvironments. Neurodegenerative disease biomarkers at pg/mL concentrations. For these projects, depletion is necessary — and we offer a workflow optimized for depth without sacrificing rigor.

Our depleted workflow uses Top12 or Top14 immunoaffinity columns to remove albumin, IgG, and additional high-abundance proteins, followed by off-line high-pH reversed-phase fractionation into 6 or 12 fractions per sample. Each fraction is acquired by DIA and the results are combined computationally. The tradeoff is throughput — fractionation multiplies instrument time by the number of fractions — but the gain is access to an additional order of magnitude in protein concentration. A typical depleted + fractionated plasma DIA run quantifies 2,000+ proteins, including cytokines and growth factors in the low ng/mL to pg/mL range.

A practical note for cohort studies: don't run your entire 500-sample cohort through fractionation. Instead, fractionate a representative subset (n = 20–30 per group) to identify candidate biomarkers in the deep proteome, then develop targeted proteomics PRM assays to quantify those specific candidates across the full cohort. This hybrid strategy gives you both discovery depth and statistical power without breaking your budget on fractionation.

Undepleted vs depleted cumulative coverage — depletion extends detection by roughly one order of magnitude, adding ~900 proteins in the low-abundance range.

Plasma protein biomarker ROC analysis — five individual candidates with AUC 0.72–0.88, combined panel AUC 0.91.

Differential plasma protein analysis — volcano plot showing significantly up- and down-regulated proteins between groups, with top candidates annotated by gene name.

Plasma-Specific Factors That Determine Data Quality

Plasma proteomics is uniquely sensitive to pre-analytical variables. The same patient's plasma can yield dramatically different proteomics results depending on how the blood was drawn, processed, and stored. These factors matter more than the mass spectrometer you use.

Plasma and Serum Sample Collection Requirements

Samples we accept: EDTA plasma (preferred), citrate plasma, serum. Heparin plasma is not compatible with trypsin digestion — we cannot accept heparinized samples.

Biobank samples with unknown history: Submit 5–10 representative samples for pilot quality assessment. We measure hemolysis index, peptide degradation, and protein yield to determine cohort eligibility.

Sample Type	Minimum Volume	Recommended Volume	Collection Notes
EDTA Plasma	200 μL	500 μL	Centrifuge at 2,000g × 10 min, 4°C, within 2 h of collection. Aliquot supernatant. Store at -80°C.
Citrate Plasma	200 μL	500 μL	Note: ~10% dilution from liquid anticoagulant. Centrifuge as above.
Serum	200 μL	500 μL	Allow 30 min clotting at RT before centrifugation. Note: coagulation/platelet proteins differ from plasma.
Whole Blood (EDTA)	1 mL	2 mL	We process to plasma in-house. Ship on cold packs, process within 24 h of collection.

For studies involving clinical proteomics endpoints, we provide GCP-compatible sample tracking and chain-of-custody documentation.

Plasma Proteomics Deliverables

What you receive depends on the path you choose — but every project includes pre-analytical QC.