Why Food Peptidomics?
Food peptidomics provides a direct, high-resolution view of endogenous and process-generated peptides in complex matrices. Unlike protein-only or amino-acid assays, peptidomics explains what peptides are present, at what levels, and how processing changes them. This evidence enables:
- Claim support: Quantify ACE-inhibitory, antioxidant, satiation-related, and mineral-binding peptides.
- Process optimization: Track hydrolysis, fermentation, thermal steps, and Maillard-related changes at peptide resolution.
- Allergen risk management: Detect epitope-containing peptides and digestion-resistant fragments.
- Quality differentiation: Compare lots, suppliers, and batches with quantitative peptide fingerprints.
What Makes Food Peptidomics Powerful?
Food peptidomics delivers molecular-level insights that protein or amino-acid tests miss. It links peptide identity, quantity, and modification to process and performance.
- Depth beyond proteins: Reveals functional fragments from enzymes, fermentation, and digestion.
- Quantitative precision: Targeted MRM/PRM enables absolute or relative peptide levels.
- Process traceability: Captures thermal, enzymatic, and Maillard fingerprints across batches.
- PTM visibility: Detects glycation, oxidation, deamidation, and cross-links that alter behavior.
- Bioactivity annotation: Maps ACE-inhibitory, antioxidant, calcium-binding, or satiation motifs.
Key Application Areas
Food peptidomics bridges the gap between protein hydrolysis, processing, and functional activity—quantifying peptides that shape flavor, bioactivity, and stability across the food value chain.
Functional Ingredient Discovery
Profile bioactive peptides with scientifically supported functions, such as antihypertensive (ACE-inhibitory), antioxidant, or satiation effects, to support claim substantiation in nutritional or functional food R&D.
Fermentation & Enzymatic Process Optimization
Characterize peptide release patterns from strain-specific proteolysis or enzyme hydrolysis. Use quantitative peptidomics to guide selection of microbial strains or enzyme systems for consistent performance.
Allergen & Epitope Monitoring
Track digestion-resistant or thermally stable peptide fragments that may retain allergenic epitopes. Evaluate the effect of processing, hydrolysis, or in vitro digestion on epitope exposure.
Quality Stability & Ingredient Comparison
Monitor peptide oxidation, glycation, and cross-linking as indicators of shelf-life, storage impact, or processing stress. Compare raw materials, suppliers, or batches using peptide-level fingerprints.
What We Offer: Comprehensive Food Peptidomics
Our food peptidomics platform transforms complex peptide mixtures into interpretable, quantitative datasets. Whether you're screening unknown bioactive peptides or validating known motifs, we provide data you can act on with confidence.
Discovery Peptidome Profiling (DDA/DIA)
Unbiased peptide identification across food matrices using data-dependent or data-independent acquisition (DDA/DIA). Label-free quantification included.
Targeted Peptide Quantification (MRM/PRM)
Absolute or relative quantitation of predefined peptides using triple quadrupole or Orbitrap PRM. Supports claim verification, batch release, and shelf-life tracking.
Bioactivity-Oriented Panels
Custom or prebuilt panels for key functional peptides:
ACE-inhibitory, DPP-IV, antioxidant, calcium-binding, appetite/satiety-related motifs.
ACE-inhibitory, DPP-IV, antioxidant, calcium-binding, appetite/satiety-related motifs.
Allergen & Epitope Surveillance
Sequence-level detection of digestion-resistant fragments or heat-stable epitopes in processed matrices.
Glycation & Post-Processing Modification Mapping
Detection of Amadori products, CML/CEL-modified peptides, and cross-linked lysine residues. Useful for thermal, pressure, or shelf-life impact studies.
Ingredient & Batch Comparison
Peptide fingerprints to benchmark suppliers, lot-to-lot variability, or formulation changes under different processing conditions.
Types of Peptides Detectable by Food Peptidomics
| Peptide Type | Source / Generation Mechanism | Scientific Relevance |
|---|---|---|
| Endogenous peptides | Naturally present in raw matrices (e.g., dairy, soy, meat) | Baseline nutritional content; precursor for bioactive motifs |
| Enzymatic hydrolysate peptides | Produced by proteases such as trypsin, alcalase, flavourzyme | Functional ingredient screening; bitterness vs bioactivity balance |
| Fermentation-derived peptides | Microbial proteolysis during fermentation | Strain-specific profiles; quality fingerprinting |
| Digestion-resistant peptides | Survive in-vitro gastric/intestinal digestion | Epitope persistence; in-vivo stability modeling (research-only) |
| Allergenic/epitope-bearing peptides | Peptides containing known IgE-binding motifs (research-only) | Risk screening in processed food, R&D allergen studies |
| Process-modified peptides | Altered by heat, oxidation, pressure, glycation | Indicators of shelf-life, degradation, or Maillard reactions |
| Post-translationally modified peptides (PTMs) | Oxidation, deamidation, cross-linking, glycation | Functional impact on structure, bioactivity, and flavor |
| Bioactive peptide motifs | Known functional sequences (e.g., ACE-I, DPP-IV inhibitors) | Health-related claims; functional product formulation |
Notes:
- Quantitation of these peptides is matrix- and sequence-dependent. We use DIA/DDA for discovery and MRM/PRM for targeted quantification.
- Peptides are annotated against public databases and motif libraries where applicable (e.g., BIOPEP-UWM, IEDB, MilkAMP).
Platform Advantages
High-Sensitivity Peptide Detection
Detects low-abundance peptides down to ng/mL levels using Orbitrap Exploris™ 480 and timsTOF Pro with diaPASEF, even in complex food matrices.
Comprehensive Modification Profiling
Simultaneously identifies glycation, oxidation, deamidation, and cross-linking events without additional enrichment workflows.
Matrix-Tolerant Sample Handling
Optimized protocols for high-fat, high-salt, or protein-dense food samples—including dairy, meats, fermented products, and plant-based isolates.
Flexible Quantification Modes
Supports both untargeted (DDA, DIA) and targeted (MRM, PRM) acquisition strategies tailored for discovery, validation, or batch QC.
Accurate Peptide-Level Fingerprinting
Delivers reproducible peptide quantitation with CVs ≤10% (targeted) and ≤15% (LFQ), enabling lot-to-lot or formulation comparisons.
Low Sample Input Compatibility
Effective from as little as 1–5 g solid or 20–50 mL liquid food matrices; suitable for limited sample availability or formulation prototypes.
Step-by-Step Food Peptidomics Workflow
Study Setup
Define sample type, target peptides, and comparison strategy.
Sample QC
Assess physical-chemical properties and potential matrix interference.
Extraction & Cleanup
Precipitate proteins, remove lipids/salts, enrich peptide fractions
LC–MS/MS
DDA/DIA for discovery; PRM/MRM for targeted quant with labled standards
Analysis & Interpretation
Identify and quantify peptides, localize PTMs, map functional motifs and process-induced changes
1
Study Design & Project Setup
Define matrix types (e.g., raw, cooked, fermented), peptide targets (bioactive, allergenic, PTM-modified), and study comparisons. Establish control groups, spike-in strategies, and analytical acceptance criteria.
2
Sample Intake & Pre-Analysis QC
Perform matrix evaluation (pH, salinity, lipids), homogenization, and interference check. Confirm sample integrity and store under standardized conditions. Pre-screen using turbidity and total protein assays.
3
Extraction & Sample Preparation
Use optimized protocols for protein precipitation and desalting (e.g., C18, HILIC). Include optional steps like lipid removal or hydrophilic enrichment for small peptides or modified residues (glycated, oxidized).
4
LC–MS/MS Acquisition
- Discovery mode: Data-Dependent (DDA) or Data-Independent Acquisition (DIA/DIA-NN) with 30–120 min C18 gradients.
- Targeted mode: Scheduled PRM/MRM with isotope-labeled standards using Orbitrap or triple quadrupole platforms.
5
Peptide Identification & Quantification
Conduct database and de novo searches with PTM localization (e.g., glycation, CML, oxidation). Apply FDR ≤ 1%. Quantify using label-free or absolute calibration, normalize with iRT and injection drift correction.
6
Bioinformatics & Reporting
Interpret sequences for functional motifs (e.g., antioxidant, ACE-inhibitory), map PTMs and degradation markers, and correlate changes with processing steps. Deliver annotated peptide tables, volcano plots, and mechanistic diagrams.
High-Resolution Instrumentation for Food Peptidomics
At Creative Proteomics, our food peptidomics workflow is built on cutting-edge mass spectrometry platforms optimized for short, modified, and low-abundance food-derived peptides. From discovery profiling to targeted quantification, we deliver deep peptidome coverage with high reproducibility across complex matrices such as hydrolysates, fermented foods, and plant/animal extracts.
Our integrated platform combines Orbitrap Exploris™, timsTOF Pro (diaPASEF), and triple quadrupole systems to meet the analytical demands of both research and industrial peptide analysis.
Technical Highlights
- High-Resolution Orbitrap MS
Full MS at up to 120k resolution with ≤3 ppm mass accuracy using lock-mass calibration. - Ion Mobility Separation (timsTOF)
diaPASEF acquisition with >100 Hz MS/MS rate and CCS filtering for dense food matrices. - Flexible Acquisition Modes
Supports DDA/DIA for discovery and PRM/MRM for targeted quantification. - Low Detection Limits
Achieves ng/mL-level LOQs with internal standards and optimized extraction; CVs typically ≤10%. - Wide Dynamic Range
105 (discovery) and >106 (targeted), suitable for major and trace-level peptides. - PTM and Processing Modification Detection
Confident identification of glycation, oxidation, deamidation, and cross-links without enrichment. - Integrated QC System
Includes iRT calibration, blank/carryover checks, and pooled QC with drift correction.
Orbitrap Exploris™ 480
(Fig from Thermo Scientific)
Q Exactive HF-X
(Fig from Thermo Fisher)
timsTOF Pro
(Fig from Bruker)
Triple Quad™ 6500+
(Fig from Sciex)
Instrument Capability Overview
| Feature | Orbitrap Exploris™ / HF-X | timsTOF Pro (diaPASEF) | Triple Quadrupole (6500+) | Orbitrap PRM Mode |
|---|---|---|---|---|
| Scan Speed | ~40 Hz | >100 Hz | N/A (point-to-point) | ~10–20 Hz |
| MS/MS Coverage | >90% | >90% | Targeted only | High |
| PTM Sensitivity | High (glycation, oxidation, etc.) | High + CCS | Moderate (only if targeted) | High |
| Quantification Mode | Label-free, DIA | Label-free, DIA | MRM with isotope standards | PRM with accurate mass |
| LOQ Sensitivity | ~low ng/mL (discovery) | ~low ng/mL (DIA) | ng/mL to sub-ng/mL | ~low ng/mL |
| Dynamic Range | >105 | >105 | >106 | >105 |
| Best Use Case | Untargeted discovery, PTM mapping | High-throughput DIA profiling | Absolute quantification of known peptides | High-specificity quant of validated targets |
| Sample Input | 1–5 g solids / 20–50 mL liquid | Same | Matrix matched, ~1–10 mL or extract | Same |
Sample Requirements for Food-Derived Peptide Profiling
| Matrix Type | Minimum Amount* | Container | Preparation Notes | Storage & Shipping |
|---|---|---|---|---|
| Powders (protein isolates, hydrolysates) | 2–5 g | Sterile screw-cap tube | Provide enzyme program/process info if available. | Store at 2–8 °C dry; ship cold pack. |
| Liquids (milk, beverages, broths) | 50–100 mL | Sealed polypropylene bottle | Avoid thickeners/preservatives when possible. Record pH. | 2–8 °C; ship cold pack. |
| Fermented products | 50–100 g or mL | Sterile container | Record strain/process parameters; avoid live overgrowth. | 2–8 °C; ship cold pack; avoid freezing if carbonated. |
| Meat/Plant tissues | 50–100 g | Whirl-Pak®/cryovial | Trim bones/peels; note treatment (thermal/pressure). | -20 °C; ship on dry ice. |
| Oils/High-fat matrices | 20–50 mL | Amber vial | Provide antioxidant info; minimize headspace. | 2–8 °C; ship cold pack. |
| Gastrointestinal digests (in-vitro models) | 20–50 mL | Screw-cap tube | Clarify enzyme recipe and time points. | -20 °C; ship on dry ice. |
*If material is scarce, contact us for low-input options. Avoid antimicrobial preservatives. Document pH and key processing parameters for best results.
Demo Results
Peptide Intensity Heatmap with Hierarchical Clustering
MS/MS Spectrum of a Representative Bioactive Peptide
Peptide Modification Distribution Plot
Volcano Plot for Differential Peptidome Profiling
Deliverables | What You Will Receive
- Raw & Peak Data
LC-MS/MS raw files (e.g., *.raw,.d) and processed peak lists (.mzML, *.mgf). - Peptide Identification
Annotated peptide lists with sequence, PTMs, precursor info, and confidence metrics (FDR/q-value). - Quantitative Results
Peptide intensity matrix across samples, differential analysis (fold change, p-value), CV%, and key statistical plots (e.g., PCA, volcano). - Precursor Protein Mapping
Links mature peptides back to their prohormone or precursor protein. - High-Quality Visuals
Publication-grade images: heatmaps, spectra, PTM distribution, and clustering plots (PNG/PDF/SVG formats). - Summary Report (PDF)
Method overview, QC stats, modification profiles, major findings, and optional biofunctional insights (e.g., via BIOPEP).
When should I choose DIA/DDA discovery vs. PRM/MRM targeting? +
Use DIA/DDA to map the peptide landscape and nominate candidates; switch to PRM/MRM when you need high-specificity quantification for predefined peptides, batch release, or longitudinal monitoring. We often run both in a staged plan.
How do you control identification confidence for complex food matrices? +
We apply peptide- and protein-level FDR control, retention-time iRT alignment, accurate-mass/fragment ion checks, and spectrum-level annotation for key peptides; targeted assays add co-elution with isotope-labeled standards.
How do you distinguish between functional peptides and random digestion fragments? +
We integrate sequence motif analysis, known bioactivity databases, and digestion-resistance scoring to highlight peptides with potential bioactive relevance.
Can you quantify bioactive motifs (ACE-I, DPP-IV, antioxidant) and track processing modifications in the same run? +
Yes. Discovery datasets capture motif-bearing peptides and modification signatures; validated targets are confirmed by PRM/MRM with isotope standards when available.
How do you handle matrix effects from fat, salts, or fermentates? +
By matrix-tuned extraction (precipitation + SPE), optional lipid removal or HILIC enrichment, and instrument methods with ion-mobility or high-resolution windows; QC blanks and pooled controls verify suppression is controlled.
Can you compare suppliers or lots in a statistically robust way? +
Yes—study designs include replicates per lot, pooled-QC tracking, and predefined thresholds for CV and effect size, yielding defensible peptide fingerprints for procurement decisions.
How do you differentiate true PTMs from artifacts such as oxidation during prep? +
We separate biological PTMs from artifacts using controlled extraction, replicate evidence, diagnostic ion patterns, retention-time behavior, and orthogonal checks (e.g., HILIC enrichment, open-mod searches with filters).
How do you ensure cross-batch comparability over time? +
Pooled-QC samples, RT-locking, instrument performance checks, and drift correction enable longitudinal trending and lot-to-lot comparability.
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