Affinity panels measure the proteins you pick in advance. Mass spectrometry finds the ones you didn't think to ask about: thousands of proteins per sample, no antibodies, in tissue, cells, FFPE, plasma and serum. We run it on a Thermo Orbitrap Astral and include the analysis.
Data-independent acquisition on a long gradient, for the most complete proteome we can get from 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 gives up some depth in exchange for much higher throughput, which is what 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.
Albumin and immunoglobulins make up most of the protein in blood and bury nearly everything clinically interesting beneath them. A nanoparticle enrichment step before digestion compresses that dynamic range, so lower-abundance plasma proteins become measurable rather than theoretical.
Site-level quantification of phosphorylation after 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 barely moves but the network does.
Our mass spectrometry work runs on the Orbitrap Astral, which pairs a high-resolution quadrupole and Orbitrap with the Astral analyzer. That combination is what lets deep coverage and precise quantitation happen in the same run rather than as a trade-off between them.
Instrument specifications per Thermo Fisher Scientific. Results depend on sample quality and type.
Every project is scoped before samples move. Study design, randomization and batch structure are settled up front rather than discovered in the data afterwards.
We run both, so we have no reason to steer you toward one or the other. 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 | Good, though low-abundance plasma proteins remain difficult | Down to fg/mL, reaching cytokines mass spec usually misses |
| Sample types | Tissue, cells, FFPE, microorganism, plant, plasma, serum | Mainly biofluids: plasma, serum, CSF, urine |
| Modifications | Yes, phosphorylation and other PTMs at site level | No |
| Sample volume | More input needed | 1 to 4 µL |
| Cross-study comparability | Depends on batch design and processing | Good; NPX is widely comparable across published studies |
| Typical use | Tissue and cell biology, mechanism, PTM signaling, broad discovery | Clinical cohorts, blood biomarker discovery, longitudinal studies |
Many studies do well with 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 person as your point of contact.
Tell us about the samples and the question. We'll recommend an approach and send a quote within one business day.
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