Peptide Analysis Service

Peptide Testing Services — Purity, Identity & Stability Analysis

Comprehensive analytical characterization for synthetic peptides. Purity, identity, amino acid composition, peptide content, impurity profiling, and structural confirmation — all from a single laboratory.

HPLC Purity LC-MS Identity Amino Acid Analysis Impurity Profiling

Testing Scope

Six categories of analytical testing for synthetic peptides

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Purity

RP-HPLC, UPLC, and SEC for quantitative purity determination.

Identity

LC-MS, MALDI-TOF, and ESI-MS for molecular weight confirmation.

Composition

Amino acid analysis and peptide content by UV absorbance.

Impurities

TFA, counterion, and residual solvent profiling.

Single Lab

All tests performed in one facility — no multi-vendor coordination.

Raw Data

Instrument-generated chromatograms and spectra, not hand-typed numbers.

Flexible

Order a single test or a full panel. No minimum requirements.

Service Details

Workflow

Platform

Advantages

Applications

Samples

Deliverables

Case Study

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Why Peptide Testing Matters

Synthetic peptides are central to drug discovery, vaccine development, epitope mapping, and structural biology. However, synthesis is rarely error-free — deletion sequences, incomplete deprotection, oxidation byproducts, and residual counterions can all compromise downstream results.

Reliable analytical testing confirms that the peptide in your vial matches the sequence you designed and meets the purity threshold your experiment requires. Without it, time and resources are spent troubleshooting assays that fail not because the hypothesis was wrong, but because the peptide was not what it was assumed to be.

Creative Proteomics provides a range of peptide testing services designed for analytical characterization and quality verification. Every test is supported by instrument-generated data — raw chromatograms, mass spectra, and integration parameters — enabling confident go/no-go decisions on peptide batches.

Scientist reviewing an HPLC chromatogram on a laboratory monitor, with peptide structural diagrams visible.

Comprehensive Peptide Testing Services

Six categories of analytical testing, each backed by instrument-generated data — raw chromatograms, mass spectra, and integration parameters. Select individual methods or combine them into a customized characterization panel.

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Peptide Purity Analysis

Purity is the single most requested QC parameter for synthetic peptides. A purity measurement tells you what percentage of the sample is your target peptide versus side products such as deletion sequences, incomplete deprotection artifacts, or oxidation byproducts.

RP-HPLC — standard purity determination; C18 column with water/acetonitrile gradient; detects impurities ≥ 0.1%
UPLC — high-resolution separation for sub-1% impurity resolution; detects impurities ≥ 0.05%
SEC — aggregate, dimer, and oligomer detection from ~0.5%; complementary to RP-HPLC

Category 01

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Identity & MW Confirmation

HPLC purity quantifies how much of the sample is the target compound; identity confirmation verifies it is the correct molecule. Mass spectrometry pairs both measurements in a single, definitive workflow.

LC-MS — combined separation + mass detection; purity and identity in one run; mass accuracy ≤ 5 ppm
MALDI-TOF MS — rapid screening; ideal for peptides above 2 kDa and high-throughput batch analysis; accuracy ≤ 50 ppm
ESI-MS — accurate mass via direct infusion; detects multiple charge states; accuracy ≤ 10 ppm

≤5 ppm LC-MS HR-MS

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Amino Acid Analysis

An MS-orthogonal method that verifies peptide composition at the residue level. Acid hydrolysis breaks the peptide into constituent amino acids, which are then derivatized, separated, and quantified against internal standards.

Composition verification — molar ratios compared to theoretical values for each residue
Leu/Ile resolution — AAA distinguishes isobaric residues that MS alone cannot differentiate
Peptide content — provides quantitative peptide content (mg peptide / mg powder) from total amino acid mass

Category 03

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Peptide Content Determination

Peptide content adds a quantitative dimension to HPLC purity. A peptide can be 98% pure by HPLC but contain only 70% peptide by weight — the remaining mass is water, TFA, and residual salts invisible to UV detection. Content determination is essential for accurate dosing in biological assays.

UV 280 nm — quantifies Trp/Tyr-containing peptides using molar extinction coefficients
UV 214 nm — universal peptide bond absorbance for peptides lacking aromatic residues; standard curve calibration

Category 04

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Impurity & Counterion Profiling

Synthetic peptides retain counterions from cleavage and residual solvents from purification. TFA, the most common counterion, can constitute 10–25% of the powder weight. Characterizing these non-peptide components helps ensure reproducible solubility, bioactivity, and stability across batches.

TFA content — ion chromatography or ¹⁹F NMR (w/w %)
Acetate / acetic acid — ion chromatography or HPLC
Residual solvents — headspace GC-MS or GC-FID, following USP <467>
Counterion screening — Cl⁻, Na⁺, K⁺, acetate by ion chromatography

Category 05

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Sequencing & Structural Confirmation

When mass spectrometry alone cannot resolve the full sequence — with novel peptides, combinatorial libraries, or sequences containing unusual modifications — tandem MS/MS provides residue-by-residue confirmation.

MS/MS de novo sequencing — CID and HCD fragmentation; confirms amino acid order without database reference
Disulfide bond analysis — non-reducing MS detects disulfide-linked peptides; reduction, alkylation, and re-analysis confirm pairing patterns

Category 06

From Purity to Full Characterization — Complementary Testing

HPLC purity provides the essential first measurement of peptide quality. The tests below extend this foundation, addressing questions that a purity determination alone was not designed to answer.

Peptide content and counterion profiling — what else is in the powder?

A peptide can be >98% pure by HPLC and still contain only 70% peptide by weight. The remaining 30% — water, TFA, and residual salts — is invisible to UV detection but directly affects dosing accuracy in biological assays.

Peptide content determination (by AAA or UV absorbance) quantifies the actual peptide per milligram of powder. Counterion profiling (by ion chromatography or ¹⁹F NMR) measures TFA, acetate, and chloride levels that can vary significantly across synthesis batches even when HPLC purity is identical.

Together, these measurements enable accurate dose normalization — especially important for multi-batch studies, dose-response experiments, and pre-formulation characterization.

Identity confirmation and aggregation — is it the right molecule, and is it intact?

HPLC purity quantifies how much UV-absorbing material is the target peak, but it does not confirm the peak corresponds to the intended sequence. Deletion sequences, incompletely deprotected intermediates, and isobaric substitutions can co-elute with the target peptide. LC-MS compares the observed molecular weight to the theoretical mass for orthogonal identity verification.

For cysteine-containing peptides, non-reducing MS confirms correct disulfide bond pairing. Meanwhile, RP-HPLC conditions — organic solvent, low pH, elevated temperature — can dissociate non-covalent aggregates that reform under native aqueous conditions. SEC under native buffer detects dimers and oligomers that may affect solubility and bioactivity even when the HPLC chromatogram appears clean.

For customers who require HPLC purity as a standalone measurement, we offer dedicated peptide purity analysis. Each complementary test can be ordered separately or as part of a comprehensive panel.

How Peptide Testing Works

A straightforward process from inquiry to data delivery. Every test follows documented analytical protocols with system suitability checks, blank controls, and senior scientist review before release.

Submit Requirements

Provide your peptide sequence(s), quantity, and which tests you need. If unsure, our team recommends a panel based on your downstream application.

Receive a Proposal

We provide a test plan with methods, pricing, and an estimated timeline based on the tests selected.

Ship Your Samples

Send peptide samples (typically 1–5 mg per test panel) as lyophilized powder. Sensitive sequences may be shipped on dry ice.

Testing & Data Analysis

Samples enter the laboratory under documented protocols. All data are reviewed by a senior analytical scientist before release.

Receive Your Report

Complete analytical package: raw instrument files, processed results, and a summary Certificate of Analysis with expert interpretation.

Analytical Platforms & Data Quality

High-resolution mass spectrometry and HPLC instrumentation in a modern analytical laboratory.

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HPLC & UPLC Systems

UV/Vis and photodiode array (PDA) detection across C18, C8, and C4 stationary phases. Method conditions tailored to peptide hydrophobicity and length.

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High-Resolution Mass Spectrometers

Q-TOF and Orbitrap platforms delivering mass accuracy ≤ 5 ppm for intact mass measurement and MS/MS fragmentation. MALDI-TOF for high-throughput screening.

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Ion Chromatography & GC-MS

Quantitative counterion analysis (TFA, chloride, acetate, sodium, potassium) and residual solvent profiling by headspace GC-MS following USP <467> methodology.

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Data Quality & Integrity

System suitability testing, blank injections, and reference standards in every analytical batch. Raw instrument files archived and provided. Every report reviewed by a senior scientist before release.

Advantages of Our Peptide Testing Services

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Multi-Method, Single Lab

Run HPLC, LC-MS, AAA, and content determination in one facility. No need to coordinate multiple vendors or reconcile inconsistent results.

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Raw Instrument Data

Every chromatogram and mass spectrum is the direct instrument output — not a manually transcribed number. Full transparency and traceability.

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Expert Interpretation

Each result is reviewed by an experienced analytical scientist who flags anomalies — unusual adduct patterns, unexpected impurity peaks — and provides context.

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Traceable, Verifiable Data

Raw instrument files — chromatograms, mass spectra, integration parameters — are provided alongside processed results. Any result can be independently verified.

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Flexible Test Selection

Order a single test (e.g., HPLC purity only) or a full characterization panel. No minimum test requirements. Pay for what you need.

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Peptide-Specific Knowledge

We routinely work with challenging peptide properties: oxidation-prone sequences (Met, Cys, Trp), aggregation-prone hydrophobic peptides, low-ionization sequences, and non-standard modifications. This depth of peptide-specific experience translates to fewer method adjustments and more reliable data across diverse sample types.

When Do You Need Peptide Testing?

Common scenarios where analytical characterization of synthetic peptides is essential.

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Incoming QC

Verify that a peptide received from a synthesis vendor meets specified purity and identity before committing it to expensive biological assays.

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Batch-to-Batch Consistency

Compare purity, content, and impurity profiles across synthesis batches to identify variability and establish acceptance criteria.

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Stability Studies

Monitor purity and impurity profiles over time under different storage conditions to establish shelf-life and handling recommendations.

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Publication Support

Verified analytical data — HPLC chromatograms, MS spectra, AAA reports — to support manuscript submissions, patent filings, and grant applications.

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Pre-Formulation

Determine peptide content, counterion levels, and solubility before formulating for animal studies or cell-based assays.

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Method Development

Use our analytical data to establish QC specifications and acceptance criteria for peptide-based products or assays.

Sample Requirements for Peptide Testing

Test Panel	Sample Required	Shipping Condition	Notes
HPLC Purity Only	≥ 1 mg	- Ambient temperature	Lyophilized powder preferred. Provide peptide sequence and expected molecular weight.
Purity + MS Identity	≥ 2 mg	- Ambient temperature	Include the full sequence with any modifications (acetylation, amidation, phosphorylation, etc.).
Full Characterization Panel	≥ 5 mg	- Ambient or dry ice	For oxidation-prone sequences (Met, Cys, Trp), dry ice shipment is recommended. Include GHS/SDS if applicable.
Multi-Batch Screening	≥ 3 mg per batch	- Ambient temperature	Label each batch clearly with batch ID and synthesis date. Peptides from the same sequence can be shipped together.
Peptides in Solution	Contact us	- Dry ice or cold pack	Provide solvent composition, concentration, and pH. Compatibility with analytical systems must be confirmed before shipment.

What You Receive

Every testing project includes a complete analytical package. You receive not just summary values, but the raw instrument data that produced them — enabling independent verification.

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Raw Instrument Data Files

Original chromatograms (.d for Agilent HPLC, .raw for Thermo MS), mass spectra, and integration parameters. Not manually transcribed — direct instrument output with full traceability.

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Processed Results Tables

Purity values with peak tables, observed vs. theoretical mass comparisons, amino acid molar ratios, peptide content calculations, and impurity concentrations.

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Certificate of Analysis (CoA)

A summary of test results with methods used and instrument information — suitable for documentation and publication supporting information.

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Expert Interpretation

Post-report consultation with the analytical scientist who reviewed your data. Anomalies (unusual adducts, unexpected impurities, integration ambiguities) are flagged and discussed.

Sample Certificate of Analysis document and analytical report portfolio on a laboratory desk.

Published Research

Quantification of a Peptide Standard Using Intrinsic Tyrosine Fluorescence

Journal

Anal Bioanal Chem

Year

2016

DOI

10.1007/s00216-016-9334-1

Study Overview

Preston and Phillips (Analytical and Bioanalytical Chemistry, 2016) addressed a fundamental challenge in peptide quantification: traditional UV absorbance methods for determining peptide content cannot distinguish between the target peptide and co-eluting peptide impurities. They developed an HPLC method with intrinsic tyrosine fluorescence detection (HPLC-FD_Tyr) as an orthogonal quantification approach for a 21-residue synthetic peptide standard (Cam-iT3) and its reduced thiol form (iT3).

Background & Motivation

Absolute peptide quantification is conventionally performed by amino acid analysis, elemental analysis, or derivatization-based methods — all of which are destructive, time-consuming, or require specialized reagents.
UV absorbance at 214/280 nm is simpler but cannot discriminate between the target peptide and co-eluting impurities, leading to overestimation when impurities share the peptide backbone absorbance.
The study sought an alternative: HPLC with fluorescence detection of intrinsic tyrosine residues, which provides an MS-independent route to peptide-specific quantitation.

Analytical Methods Used

RP-HPLC with diode array (DAD) and fluorescence (FD) detection in series, using a C18 column and water/acetonitrile gradient with 0.1% formic acid.
ESI-MS and MS/MS for peptide identity confirmation and impurity characterization in the commercial peptide preparation.
UV-Vis absorbance and fluorescence spectroscopy for optical characterization of the peptide and calibrant.
Ellman's assay (DTNB derivatization) as an independent verification method for thiol content.

Key Finding

The HPLC-FD_Tyr method achieved quantification results that agreed with the Ellman's assay after correction for fluorescence response differences between the peptide calibrant (Ac-Tyr-OEt) and the peptide analyte. However, variability persisted — the study demonstrated that impurities in commercial peptide preparations complicate quantification regardless of the detection method, reinforcing the need for orthogonal approaches and well-characterized reference standards in peptide analytical workflows.

Relevance to Peptide Testing

Demonstrates why peptide content determination should accompany, not replace, HPLC purity analysis
Shows that orthogonal methods (HPLC + MS + fluorescence + chemical assay) provide complementary information
Highlights that co-eluting impurities can confound single-method quantification
Underscores the value of providing raw instrument data for independent verification

Publication Reference

Preston GW, Phillips DH. Quantification of a peptide standard using the intrinsic fluorescence of tyrosine. Anal Bioanal Chem. 2016;408(9):2187–2193. DOI: 10.1007/s00216-016-9334-1.

Frequently Asked Questions

How much peptide sample do I need to send for testing?expand_more

A standard test panel (HPLC purity + LC-MS identity + AAA) requires approximately 3–5 mg of lyophilized peptide. For fewer tests, we can work with as little as 1 mg. For multi-batch screening or full characterization panels, we recommend 5–10 mg. Contact us with your specific requirements for a precise sample requirement estimate.

What is the difference between HPLC purity and peptide content?expand_more

HPLC purity measures the percentage of UV-absorbing material that is your target peptide — it does not account for non-UV-absorbing components like water, salts, and TFA. Peptide content measures the actual weight of peptide per unit of powder weight. A peptide can be >98% pure by HPLC but contain only 70% peptide by weight. For biological assays requiring accurate dosing, both values matter. We recommend including peptide content determination alongside purity testing.

Can you test peptides with unusual modifications or non-standard amino acids?expand_more

Yes. We routinely test peptides containing phosphorylated residues (pSer, pThr, pTyr), acetylated and amidated termini, fluorescent labels (FITC, Cy dyes, TAMRA), biotin, PEG, fatty acid conjugates, D-amino acids, and cyclic peptides. Providing the full sequence and modification details at the inquiry stage helps us select the most appropriate analytical methods.

Can you help interpret unexpected or conflicting test results?expand_more

Yes. When results from different analytical methods appear to conflict — for example, high HPLC purity but low AAA recovery — our scientists investigate the root cause and provide a reconciled interpretation. Common scenarios include non-UV-absorbing contaminants inflating HPLC purity, incomplete hydrolysis affecting AAA values, and co-eluting impurities with similar retention times. Every report includes expert commentary that contextualizes results across all methods performed.

What file formats do you deliver for instrument data?expand_more

We provide instrument raw data in standard formats (e.g., .raw for Thermo MS data, .d for Agilent HPLC data) and processed reports as PDF documents. If you require specific formats for your documentation or publication, please mention this when placing your order.

Can you test peptides that are already dissolved in buffer or solvent?expand_more

We prefer lyophilized powder when possible, as it provides the most stable form for shipping and storage. If you must send peptides in solution, please contact us for specific solvent and concentration guidelines before shipment to ensure compatibility with our analytical systems.

How do you ensure the accuracy and reliability of results?expand_more

Every analytical run follows documented quality controls: system suitability testing and instrument calibration before each sample sequence, blank injections to verify system cleanliness, reference standards in every analytical batch, replicate injections for quantitative methods, and senior scientist review of every report before release. Raw instrument data files are archived and provided alongside processed results so any result can be independently verified.

Can I order a single test rather than a full panel?expand_more

Yes. There is no minimum test requirement. You can order a single test — for example, HPLC purity only — or a full characterization panel. Our technical team can also recommend the most appropriate tests based on your peptide sequence and downstream application.