Quantify what survives your sample preparation, not what you assume did.

Custom ¹³C-labeled full-length protein standards for quantitative mass spectrometry — including monoclonal antibodies, AAV capsids and individual VP proteins. Spike the standard before enrichment and sample preparation so analytical losses occur alongside your analyte.

Request a pilot standard How it works

Standards: Monoclonal antibody · AAV VLP · VP1 / VP2 / VP3
Labeling: ¹³C Arg / Lys · custom schemes available
Program: Early-access pilot engagements

Two-track comparison of an AAV quantification workflow by LC-MS/MS. Top track, without a stable isotope-labeled standard: the sample passes through affinity capture, buffer exchange and cleanup, and digestion to peptides, with losses possible at each step, and is then measured by LC-MS/MS against a calibration curve built from separate standards run at different times — more variable between runs, harder to control, higher uncertainty. Bottom track, with an AAV stable isotope-labeled standard: the labeled standard is added to the sample before affinity capture, so losses at capture, cleanup and digestion are shared by analyte and standard, and LC-MS/MS measures light and heavy peptide pairs within the same scan, correcting for those losses and yielding the endogenous concentration from a single run. — Tap to enlarge

What we make

Standards are produced to your sequence. There is no catalogue — each standard is expressed for the target it is meant to quantify.

Monoclonal antibody standards

Matched full-length labeled antibody standards for quantitative LC-MS workflows, including PK and protein-level immunocapture assays.

AAV capsid standards

Assembled isotope-labeled capsids designed to track recovery through affinity capture, buffer exchange and downstream sample preparation.

VP1 / VP2 / VP3 standards

Individually produced and quantified standards for direct measurement of capsid-protein abundance and VP stoichiometry.

Discuss your target

If the loss happens before digestion, a peptide standard never sees it.

Correct capture losses

The labeled protein enters before immunocapture or AAV affinity enrichment, presenting the same epitope to the capture ligand.

Correct preparation losses

Analyte and standard experience adsorption, cleanup and digestion together, so recovery becomes a shared denominator rather than an error term.

Measure a ratio

The light-to-heavy response converts a known standard amount into a quantitative protein measurement.

Peptide standard or protein standard

Which losses each format is physically able to correct.

	AQUA peptide	Full-length SIL protein
LC-MS variability	✓	✓
Digestion variability	—	✓
Protein-level capture	—	✓
Pre-digestion sample loss	—	✓
Transfer between matrices	—	Improved

Matrix is where an internal standard is tested hardest

Ion suppression and enhancement vary with the sample, so a correction factor established in one matrix need not hold in another² — which is why a method that moves between plasma, tissue homogenate and in-process material is the case that separates the formats. A standard that enters before capture and digestion shares more of that variation with the analyte than one added after digestion^3,6. Peptide and protein internal standards have been compared directly in this respect^4,5,6.

Matched standards compensate shared matrix effects. They do not remove all of them, and they do not correct loss that occurred before the standard was added.

Different standards solve different analytical problems. AQUA peptides¹ remain excellent standards when peptide-level rather than protein-level workflow correction is required, and have supported clinical programmes at scale⁷.

Built for controlled labeling

Avenyx uses cell-free protein synthesis to control the composition of the reaction rather than relying on a metabolically active labeling host. This creates a direct route to custom isotope-labeled proteins while avoiding many of the metabolic constraints of conventional SILAC production.

The same programmable biomanufacturing architecture under development at Avenyx Bio is being applied to analytical standards.

Learn about our technology

Tell us what you want quantified

Early-access program

We are currently evaluating a limited number of pilot projects. If another internal-standard format is better suited to your assay, we'll tell you.

No sequences are needed at this stage. A description of the target and the assay is enough for a feasibility assessment.

References

Published work cited in support of the points above. These are the work of their authors, not of Avenyx Bio.

Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. PNAS 2003;100(12):6940–6945. pnas.org
Matuszewski BK, Constanzer ML, Chavez-Eng CM. Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS. Anal Chem 2003. PubMed
Protein biomarker quantification by immunoaffinity liquid chromatography–tandem mass spectrometry: current state and future vision. Clin Chem 2020;66(2):282–301. Clinical Chemistry
Prasad B, Unadkat JD. Comparison of heavy labeled (SIL) peptide versus SILAC protein internal standards for LC-MS/MS quantification of hepatic drug transporters. Int J Proteomics 2014;2014:451510. PubMed
Li H, et al. General LC-MS/MS method approach to quantify therapeutic monoclonal antibodies using a common whole antibody internal standard, with application to preclinical studies. Anal Chem 2012;84:1267–1273. PubMed
Ravazza D, et al. Quantitative mass spectrometry-based biodistribution of monoclonal antibodies: an alternative to radio-biodistribution. Advanced Science 2026. Wiley
Huang Y, et al. Comprehensive performance evaluation of a ligand-binding assay–LC–MS/MS method for co-dosed monoclonal anti-SARS-CoV-2 antibodies (AZD7442). Bioanalysis 2024. Taylor & Francis

Full reference list