40+ years of excellence in custom synthesis and bioconjugation services.
Calculators, design tools, and educational content to support your research.
Stable isotope-labeled internal standards engineered for accurate, reproducible protein and peptide quantification by targeted LC-MS/MS.
AQUA (Absolute QUAntification) peptides are stable isotope-labeled synthetic internal standards designed for quantitative LC-MS/MS.
The heavy peptide typically matches the endogenous target sequence and closely follows its chromatographic and fragmentation behavior, while one or more 13C- and/or 15N-labeled amino acids create a defined mass shift. Measuring the heavy standard together with the native light analyte enables accurate isotope-dilution quantification.
Bio-Synthesis supports AQUA projects from target-peptide review and isotope selection through stable isotope-labeled peptide synthesis, preparative HPLC purification, LC-MS and release QC, optional amino acid analysis, custom aliquoting, and project-specific documentation.
AQUA is an application-specific standard. Stable isotope-labeled peptides describe the broader chemistry category. AQUA standards are specifically configured and characterized for quantitative mass-spectrometry workflows.
Representative chromatographic concept: the heavy internal standard and endogenous light peptide co-elute, while their distinct mass transitions allow independent integration and ratio-based quantification.
Known heavy standards support absolute or calibrated peptide and protein measurements.
Optional AAA provides orthogonal peptide-content and concentration assignment.
Preparative RP-HPLC with application-specific purity targets and analytical verification.
LC-MS, analytical HPLC, optional isotope verification, AAA, COA, and custom documentation.
Custom AQUA standards can be configured for assay development, verification, and quantitative studies across a range of LC-MS/MS workflows.
Candidate verification and panel development
Absolute or calibrated quantification
Transition-based quantitative assays
High-resolution targeted measurements
Peptide and protein bioanalysis support
Translational and method-transfer studies
From a single internal standard to larger biomarker panels, each project can be configured around the target sequence, analytical platform, required amount, and level of quantitative characterization. Our synthesis platform also supports many hydrophobic, aggregation-prone, long, cyclic, and other challenging peptide sequences encountered in quantitative proteomics.
Common options include heavy lysine, arginine, leucine, valine, isoleucine, phenylalanine, and other labeled residues using 13C and/or 15N enrichment.
LC-MS identity confirmation, analytical HPLC, optional amino acid analysis, isotope-related verification, value assignment, and project-specific release documentation.
Heavy labels can be combined with selected post-translational modifications, oxidative products, and sample-preparation modifications. See the complete modification options below.
Lyophilized or solution formats, low-bind vialing, single-use aliquots, plate formats, custom blends, and application-specific packaging.
Select a heavy residue that provides an appropriate mass shift and analytical response, then match any endogenous post-translational or sample-preparation modification required by the assay.
Common uniformly labeled amino acids are shown below. Final availability and isotopologue selection are confirmed during quotation.
† Availability note: Additional isotope-labeled amino acids, alternative isotopologues, and multiple-label combinations may be available on request. Mass difference values are nominal mass shifts. Final label selection should consider protease cleavage, isotope-envelope separation, fragment-ion design, and assay requirements.
Multiple stable isotope-labeled amino acids may be incorporated into a single peptide when a larger mass shift, improved fragment-ion coverage, or assay-specific analytical performance is required.
Heavy isotope labeling can be combined with selected post-translational, oxidative, or sample-preparation modifications when compatible with the sequence and synthesis strategy.
Site-defined phosphotyrosine (pY), phosphothreonine (pT), or phosphoserine (pS) standards for PTM quantification.
Modification-matched standards representing cysteine alkylation commonly introduced during proteomic sample preparation.
Site-defined chlorinated tyrosine standards for oxidative-stress, inflammation, and biomarker research.
N-terminal pyroglutamate standards prepared to match endogenous or process-generated cyclization states.
Oxidation-state standards for monitoring methionine sulfoxide, sample handling, or oxidative modification.
Additional post-translational and chemical modifications may be available following sequence-specific feasibility review.
‡ CAM note: Carbamidomethylated cysteine is typically used to match the analytical form generated after iodoacetamide alkylation. The requested residue position and modification state should be specified explicitly.
Design support: Bio-Synthesis can review label position, nominal mass separation, PTM state, synthesis feasibility, purification strategy, amino acid analysis requirements, and final delivery format before quotation.
Lyophilized peptide mass alone does not necessarily equal the amount of target peptide present. Water, counterions, residual salts, and other nonpeptide components can affect the true peptide content.
Optional amino acid analysis (AAA) provides an independent measurement of peptide content and supports more reliable concentration assignment for absolute quantification, assay calibration, biomarker validation, and interlaboratory method transfer.
AAA complements—but does not replace—identity and purity testing. LC-MS confirms expected molecular mass, analytical HPLC evaluates the chromatographic profile, and AAA supports quantitative value assignment.
Actual peptide content versus gross lyophilized weight
Water, salts, counterions, and residual nonpeptide mass
Preparation of accurately assigned stock solutions
Reproducibility across aliquots, batches, and laboratories
Every quantitative peptide is manufactured according to project requirements rather than restricted to a fixed catalog grade. Purity, peptide length, formulation, target concentration, total quantity, amount per aliquot, vial or plate format, analytical testing, documentation, and shipping conditions can all be tailored to the intended workflow.
These are planning examples, not fixed grades. Purity, peptide length, total quantity, amount per vial, number of aliquots, heavy amino acid, formulation, target concentration, analytical testing, documentation, and shipping conditions are selected for each project.
The workflow is configured around assay requirements, target confidence, value-assignment strategy, and final delivery format.
Sequence uniqueness, protease compatibility, liabilities, solubility, and LC-MS suitability.
Select heavy residue, mass shift, placement, enrichment, and modification state.
Sequence-specific SPPS with difficult-sequence and PTM strategies as needed.
Purification to the selected application-specific purity target.
LC-MS identity, analytical HPLC, and optional advanced characterization.
Optional amino acid analysis, assigned content, aliquoting, COA, and shipment.
Important: A synthetic AQUA peptide added after proteolysis primarily corrects for LC-MS response, sample injection, and instrument variation. It does not fully compensate for protein extraction or digestion efficiency. Extended peptides, labeled proteins, or orthogonal process controls may be more appropriate when earlier workflow steps must also be controlled.
Each method answers a different quality question. The final package should be selected according to the required confidence in identity, purity, isotope labeling, and assigned peptide content. Project-specific characterization may also include high-resolution mass spectrometry (HRMS) or other specialized methods when appropriate.
Determine target abundance using a known heavy internal standard and an appropriately validated response model.
Support transition development, retention-time confirmation, calibration, and targeted quantification on triple quadrupole platforms.
Enable high-resolution targeted measurements using matched heavy and light precursor and fragment-ion signals.
Quantify candidate biomarkers across research cohorts and support development of multiplex peptide panels.
Measure phosphorylated, acetylated, methylated, or other modified peptide forms using modification-matched standards.
Support LC-MS method development for peptide therapeutics, protein drugs, and related research analytes.
Design custom stable isotope-labeled peptides for quantitative LC-MS/MS, targeted proteomics, biomarker validation, and internal standard development.
Custom phosphopeptides and other post-translationally modified peptides for signaling studies, biomarker research, and quantitative proteomics.
High-resolution preparative HPLC purification for peptide projects requiring enhanced purity, recovery, and application-specific method development.
Comprehensive LC-MS and analytical HPLC characterization for identity confirmation, purity assessment, release QC, and project-specific documentation.
Bio-Synthesis combines more than four decades of peptide synthesis experience with flexible analytical characterization to support quantitative proteomics from early method development through biomarker validation and translational research.
Sequence uniqueness, protease compatibility, synthesis risk, isotope strategy, purification, LC-MS behavior, quantitative value assignment, packaging, and fit-for-purpose release testing.
AQUA and stable isotope-labeled peptide programs are supported by controlled synthesis, purification, analytical characterization, optional amino acid analysis, project-specific documentation, and customized packaging.
Selected references covering AQUA peptide standards, stable-isotope dilution, targeted proteomics, and quantitative mass spectrometry.
Note: References are provided for scientific background. Final assay performance depends on peptide selection, matrix, digestion, calibration model, sample preparation, LC-MS method, and validation strategy.
Trusted by biotech leaders worldwide for over 45 years of delivering high-quality, fast, and scalable synthetic biology solutions.