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Targeted Proteomics & Quantitative LC-MS Peptides

Custom peptide standards for targeted proteomics, relative quantification, biomarker verification, and absolute quantification by LC-MS/MS. Choose flexible stable isotope-labeled peptides or quantitatively characterized AQUA peptide standards based on the accuracy and documentation your assay requires.

MRM / SRM PRM DIA Biomarker Verification Absolute Quantification
Explore Peptide Options Discuss Your Project
Overview Peptide Options Selection Guide Capabilities QC & Deliverables Applications FAQ Contact
Overview

Peptide Standards Built Around Your Quantitative Workflow

Targeted proteomics depends on sequence-defined reference materials that behave like the endogenous analyte during chromatography and mass spectrometry. Stable isotope-labeled peptides provide a distinguishable heavy signal while retaining comparable chemical and chromatographic behavior.

Bio-Synthesis supports custom peptide design, stable isotope incorporation, post-translational modifications, preparative purification, formulation, aliquoting, and analytical characterization. Projects may be configured for method development, relative quantification, biomarker verification, or absolute peptide quantification.

Service Paths

Two Primary Service Paths

Select the level of quantitative characterization and documentation required for your assay. Both paths can be customized for sequence, isotope label, purity, formulation, and delivery format.

Stable Isotope-Labeled Peptides

Flexible heavy peptide standards for method development, assay optimization, relative quantification, and research-use internal standards.

AQUA Peptide Standards

Quantitatively characterized standards for absolute measurement, biomarker verification, assay qualification, and higher-confidence LC-MS/MS workflows.

Primary Services

Choose the Quantitative Peptide Solution That Fits Your Assay

Both service categories are fully customizable. The distinction is based on the depth of quantitative characterization, formulation, and documentation selected for the project.

SIL

Stable Isotope-Labeled Peptides

Custom heavy peptides for relative quantification, method development, targeted assay optimization, and use as internal standards.

  • Flexible heavy amino-acid selection
  • Single or multiple isotope labels
  • Light and heavy peptide pairs
  • Optional PTMs and custom modifications
  • Purity and QC tailored to the project
AQUA

AQUA Peptide Standards

Stable isotope-labeled standards configured for absolute quantification, biomarker verification, assay qualification, and quantitative LC-MS/MS workflows.

  • Quantitative amino acid analysis options
  • Peptide-content or concentration assignment
  • Custom formulation and aliquoting
  • LC-MS and analytical HPLC documentation
  • Enhanced quantitative support packages
Selection Guide

Which Peptide Standard Should You Choose?

Start with the analytical question your assay must answer. Bio-Synthesis scientists can then recommend the isotope-labeling strategy, purity, quantitative characterization, and delivery format.

Choose Stable Isotope-Labeled Peptides

For discovery studies, method development, transition optimization, relative quantification, or projects where a flexible heavy internal standard is the primary need.

Choose AQUA Peptides

For absolute quantification, biomarker verification, assay qualification, multi-site studies, or workflows requiring peptide-content assignment and expanded documentation.

Request a Custom Configuration

For modified peptides, difficult sequences, multiple labels, plate-ready aliquots, custom concentrations, specialized formulations, or project-specific QC.

Project Requirement Stable Isotope-Labeled Peptides AQUA Peptide Standards
Relative quantification or assay development Well suited Available when enhanced characterization is desired
Absolute peptide quantification Available with project-specific quantitative characterization Primary application
Heavy amino-acid selection Custom Custom
PTMs and multiple modifications Available by sequence and chemistry review Available by sequence and chemistry review
Amino acid analysis Optional Commonly selected for quantitative assignment
Formulation and aliquoting Custom Custom, including ready-to-use configurations
Documentation package Selected to project requirements Expanded quantitative documentation available
Integrated Workflow

From Peptide Design to Quantitative LC-MS/MS

Phase 1 Plan the Assay Define the biological target and design the correct quantitative standard before manufacturing begins.

Assay & Target Review

Review the target protein, protease strategy, analyte form, matrix, transitions, and quantitative objective.

Peptide & Label Design

Select the proteotypic sequence, isotope position, PTMs, matched light peptide, and synthesis configuration.

Phase 2 Manufacture the Standard Use sequence-specific synthesis and purification strategies to produce the required peptide configuration.

Custom Synthesis

Manufacture the peptide at a project-appropriate scale using sequence-specific chemistry and modification strategies.

Preparative Purification

Apply preparative HPLC or another suitable purification strategy to reach the selected purity target.

Phase 3 Characterize & Release Confirm identity and purity, assign quantitative value when required, and prepare final release documentation.

Identity & Purity QC

Confirm identity and purity using selected LC-MS, LC-MS/MS, HRMS, analytical HPLC, or UPLC methods.

Quantitative Assignment

Perform amino acid analysis, peptide-content determination, concentration verification, or isotope assessment as required.

Release, COA & Delivery

Complete formulation, aliquoting, analytical reporting, Certificate of Analysis, and project-specific release documentation.

Platform Capabilities

Custom Chemistry, Quantitative Characterization, and Flexible Delivery

Projects are not limited to predefined peptide lengths, quantities, or aliquot formats. Final feasibility depends on sequence, modifications, solubility, purity target, and analytical requirements.

13C

Heavy Labeling

Common heavy amino acids, alternative isotopologues, and multiple-label designs for assay-specific mass shifts.
PTM

Modified Standards

Phosphorylation, carbamidomethylation, oxidation, pyroglutamate, chlorotyrosine, and other modifications by review.
QC

Analytical QC

LC-MS, analytical HPLC, amino acid analysis, HRMS, isotope verification, and customized documentation.
Rx

Custom Formulation

Lyophilized or solution delivery, target concentration, custom buffer, counterion selection, and aliquoting.
L/H

Light/Heavy Pairs

Matched unlabeled and stable isotope-labeled peptide standards for calibration and assay development.
D

Difficult Peptides

Support for many hydrophobic, aggregation-prone, long, cyclic, or multi-modified peptide sequences.
96

Custom Aliquoting

Single vials, multiple aliquots, plate-ready formats, and customer-defined amount per container.
COA

Documentation

Certificate of Analysis, chromatograms, mass spectra, AAA data, and project-specific release packages.
Flexible Manufacturing & Delivery

Configure the Standard Around the Assay—not the Other Way Around

Sequence, isotope strategy, purity, scale, formulation, concentration, packaging, and analytical documentation can be combined into a project-specific configuration.

Sequence & Chemistry

Custom sequence, proteotypic peptide selection, heavy residue placement, multiple labels, PTMs, and difficult-sequence review.

Purity & Scale

Research through production-oriented quantities, with purity and purification strategy selected according to assay needs and sequence feasibility.

Formulation

Lyophilized or solution delivery, customer-specified solvent or buffer, target concentration, counterion options, and solubility considerations.

Packaging

Single vial, multiple aliquots, plate-ready formats, light/heavy pairs, mixtures, custom labeling, and amount per container.
Analytical Characterization & Release QC

Fit-for-Purpose QC for Quantitative Peptide Standards

Every targeted proteomics project has different analytical requirements. Bio-Synthesis can configure the release package for discovery research, assay development, biomarker verification, translational studies, or absolute quantification without forcing the project into a fixed catalog grade.

ID

Identity Confirmation

  • LC-MS mass confirmation
  • LC-MS/MS sequence support
  • High-resolution MS (HRMS)
  • Project-specific mass analysis
%

Purity Assessment

  • Analytical HPLC
  • UPLC where appropriate
  • UV chromatographic assessment
  • Purity reporting by selected method
AAA

Quantitative Characterization

  • Amino acid analysis (AAA)
  • Peptide-content determination
  • Concentration verification
  • Isotope incorporation assessment
+

Additional Testing

  • Counterion analysis
  • Solubility evaluation
  • Stability studies, project dependent
  • Custom analytical reports
L/H

Light/Heavy Pairs

Matched unlabeled and stable isotope-labeled peptide standards for calibration and assay development.
D

Difficult Peptides

Support for many hydrophobic, aggregation-prone, long, cyclic, or multi-modified peptide sequences.
96

Custom Aliquoting

Single vials, multiple aliquots, plate-ready formats, and customer-defined amount per container.
COA

Documentation

Certificate of Analysis, chromatograms, mass spectra, AAA data, and project-specific release packages.
Typical Deliverables

Documentation and Material Prepared for Your Workflow

Deliverables are selected according to the project configuration and intended research use.

  • Lyophilized peptide or solution
  • Certificate of Analysis (COA)
  • Analytical HPLC or UPLC chromatogram
  • LC-MS or LC-MS/MS report
  • AAA or peptide-content report, when selected
  • Isotope assessment, when selected
  • Custom concentration and aliquot record
  • Project-specific release documentation
Applications

Designed for Modern Targeted Proteomics Workflows

MRM and SRM assay development
Parallel reaction monitoring
DIA verification workflows
Biomarker verification and validation
Absolute protein quantification
Pharmacokinetic and bioanalytical research
PTM quantification
Assay transfer and inter-laboratory studies
Translational research
Why Bio-Synthesis?

A Custom Manufacturing Partner for Quantitative Proteomics

Bio-Synthesis combines more than four decades of peptide synthesis experience with flexible analytical and formulation services. Each project is configured around the scientific question rather than restricted to a catalog specification.

40+
Experienced Peptide Team

Long-standing expertise in custom peptide synthesis, modification, purification, and analytical support.

∞
Custom, Not Fixed

Sequence, label, purity, quantity, concentration, formulation, aliquoting, and QC can be tailored.

A
Integrated Analytics

Manufacturing and characterization can be coordinated within a single project plan.

S
Scientist Support

Technical consultation for peptide selection, isotope placement, PTMs, and quantitative workflow design.

Scientific Consultation & Quote

Need Help Selecting a Quantitative Peptide Standard?

Our scientists can help determine whether a stable isotope-labeled peptide or an AQUA configuration best fits your assay, then recommend the sequence, isotope-labeling strategy, post-translational modification, purity, formulation, aliquoting, and analytical package.
Request a Quote Consult a Peptide Scientist

Need help before quoting?

Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)

Information for Project Review

  • Target protein and organism
  • Peptide sequence and PTM state
  • Heavy residue and label position
  • Quantity and purity target
  • Relative or absolute quantification goal
  • Aliquot, solution, plate, or mixture format
  • MRM, SRM, PRM, DIA, or other acquisition method
  • Documentation and shipping requirements

What We Review

Sequence uniqueness, protease compatibility, synthesis risk, isotope strategy, purification, LC-MS behavior, quantitative value assignment, packaging, and fit-for-purpose release testing.

Quality Systems

Quality Systems & Manufacturing Support

QMS

ISO-Supported Peptide Manufacturing

Targeted proteomics, stable isotope-labeled peptide, and AQUA programs are supported by controlled synthesis, purification, analytical characterization, documentation, traceability, and project-specific packaging.

ISO 9001:2015 Quality management system
ISO 13485:2016 Medical-device quality framework
ISO 14001 Environmental management system
Quantitative Characterization HPLC or UPLC, LC-MS, optional HRMS and AAA, peptide-content assignment, and certificate of analysis

Targeted Proteomics & Quantitative LC-MS Peptides FAQ

FAQ

What is the difference between a stable isotope-labeled peptide and an AQUA peptide?
A stable isotope-labeled peptide is a heavy internal standard. An AQUA peptide is generally configured with the quantitative characterization, content assignment, formulation, and documentation needed for absolute quantification.
Can you provide matched light and heavy peptide pairs?
Yes. Matched unlabeled and stable isotope-labeled peptides can be synthesized for calibration curves, method development, system suitability, and assay verification.
Can PTMs be combined with heavy isotope labels?
Yes, many post-translational modifications and chemical modifications can be combined with stable isotope labeling. Feasibility is reviewed for each sequence and modification pattern.
Is amino acid analysis required for every project?
No. AAA is selected when quantitative peptide-content assignment is important. Research-stage standards may use a lighter analytical package, while absolute quantification projects commonly benefit from AAA.
Can you prepare custom concentrations and aliquots?
Yes. Total quantity, amount per vial, number of aliquots, target concentration, solvent system, and packaging format can be customized for the project.
What information is helpful for a quote?
Please provide the peptide sequence, desired isotope label, PTMs, quantity, purity, formulation, aliquot plan, analytical requirements, and intended LC-MS/MS workflow.
More FAQ'sAll FAQ's
Scientific Background & Recommended Reading

Recommended Reading

Selected references covering stable-isotope dilution, AQUA peptide standards, targeted proteomics, and quantitative mass spectrometry.

  1. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proceedings of the National Academy of Sciences USA. 2003.
  2. Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods. 2005.
  3. Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular Systems Biology. 2008.
  4. Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nature Methods. 2012.
  5. Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-Orbitrap mass spectrometer. Molecular & Cellular Proteomics. 2012.

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.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45 years of delivering high-quality, fast, and scalable synthetic biology solutions.

Greetings, Researchers,

Please be advised that any information, guidelines, write-ups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the design of products intended for their experiments before submitting
their designs to Biosynthesis for production feasibility review.
Thank you for your understanding.

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