Affinity panels measure the proteins you choose in advance. Mass spectrometry finds the ones you didn't know to ask about — thousands of proteins per sample, no antibodies required, across tissue, cells, FFPE, plasma, and serum.
Data-independent acquisition on a long gradient, for the most complete proteome we can reach in a given sample type. This is the right choice for discovery work where a protein you miss is a finding you miss — mechanism studies, tissue and cell biology, and any experiment where you don't yet know what you're looking for.
A shorter gradient trades some depth for substantially higher throughput, which makes large sample numbers affordable. Built for population-scale studies, treatment arms, and screens where consistency across hundreds of samples matters more than reaching the deepest possible proteome in any one of them.
Blood proteomics is dominated by albumin and immunoglobulins, which bury almost everything clinically interesting beneath them. A nanoparticle enrichment step ahead of digestion compresses that dynamic range, so lower-abundance plasma proteins become measurable rather than theoretical.
Site-level quantification of protein phosphorylation following phosphopeptide enrichment. Use it when the biology lives in signaling state rather than expression level — kinase inhibitor response, pathway activation, and mechanism-of-action work where total protein abundance barely moves but the network does.
Our mass spectrometry services run on the Orbitrap Astral, which combines a high-resolution quadrupole filter, an Orbitrap analyzer, and the Astral analyzer. The combination is what makes deep coverage and precise quantitation achievable in the same run rather than as a trade-off.
Instrument specifications per Thermo Fisher Scientific. Results vary with sample quality and type.
Every project is scoped before samples move — study design, randomization, and batch structure are decided in advance rather than discovered in the data afterwards.
We run both, so we have no reason to steer you toward either one. These are the trade-offs we'd walk through with you on a call.
| Mass spectrometry | Olink / NULISA | |
|---|---|---|
| Target selection | Unbiased — you find proteins you weren't looking for | Predefined panel — you measure what the panel covers |
| Sensitivity | Strong, though low-abundance plasma proteins remain challenging | Down to fg/mL — reaches cytokines mass spec typically misses |
| Sample types | Tissue, cells, FFPE, microorganism, plant, plasma, serum | Primarily biofluids — plasma, serum, CSF, urine |
| Modifications | Yes — phosphorylation and other PTMs at site level | No |
| Sample volume | Higher input required | 1–4 µL |
| Cross-study comparability | Depends on batch design and processing | Strong — NPX is broadly comparable across published studies |
| Best for | Tissue and cell biology, mechanism, PTM signaling, broad discovery | Clinical cohorts, blood biomarker discovery, longitudinal studies |
Many studies benefit from both: mass spectrometry to generate candidates in tissue, then a targeted affinity panel to validate them in plasma across a larger cohort. We can design and run that end to end, on the same samples, with one point of contact.
Tell us about your samples and your question — we'll recommend an approach and get you a quote within 24 hours.
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