Peptidomics
Peptidomics
What Is Peptidomics? Why Peptide Profiling Is Essential
MetwareBio offers a specialized peptidomics service that leverages cutting-edge 4D label-free LC-MS/MS technology to achieve highly sensitive and accurate peptide detection. Using the ddaPASEF acquisition mode, the system captures low-abundance endogenous peptides with exceptional resolution and efficiency. Our flexible sample preparation workflow supports a wide range of species and sample types—from cells and tissues to various biological fluids—ensuring robust peptide extraction across diverse research needs. We employ comprehensive and professional bioinformatics pipelines to transform complex raw data into actionable biological insights, including peptide identification, quantitative profiling, functional annotation, pathway enrichment, and integrative interpretation, to support high-impact scientific discoveries.
Comprehensive Peptide Analysis Workflow: From Discovery and Validation to Clinical Translation (Hellinger et al., 2023)
Why Choose MetwareBio for Endogenous Peptide Analysis?
Workflow for LC-MS/MS Peptidomics Service
Peptidomics Data Deliverables
Experience in Peptidomics Analysis Service
Number of peptides identified from various medical, animal and plant samples via label-free peptidomics
Applications of Peptide Profiling
Peptidomics provides in-depth insights into peptide-level changes in human diseases. By identifying and quantifying peptides involved in signaling pathways, peptidomics aids in biomarker discovery, understanding disease mechanisms, and identifying potential therapeutic targets in fields such as oncology, neurology, and metabolic disorders.
Peptidomics is a powerful tool for studying the functional dynamics of microbial systems, including virulence factor regulation, stress response, and metabolic adaptation. It plays a key role in understanding host–pathogen interactions, immune responses, and microbial adaptation in infection models, offering new avenues for antimicrobial therapy development.
In plant systems, peptidomics helps explore peptide functions in growth, stress responses, and hormone signaling. It provides critical insights for agricultural biotechnology, enabling molecular breeding, stress resistance enhancement, and improved crop traits, contributing to sustainable agricultural practices.
Peptidomics plays a vital role in understanding the peptide profiles involved in nutrition, metabolism, and health. It aids in studying how dietary peptides influence metabolic pathways, gut microbiota, and immune function. This approach is valuable for developing nutritional interventions, functional foods, and personalized health strategies.
By integrating peptidomics with proteomics and metabolomics, we gain a systems-level understanding of gene function, cellular processes, and regulatory networks. This holistic approach enables the study of biological pathways across various species and conditions, driving advances in functional genomics, systems biology, and multi-omics research.
Cast Study: Label-Free Peptidomics in Food Nutritional Research
In a study recently published in Food Chemistry titled "Leveraging ultra-micro crayfish shell powder to modulate protein digestion and health benefits in silver carp surimi", researchers explored the effects of ball-milled crayfish shell powder (MD) and ball milling combined with irradiation crayfish shell powder (MID) on the protein digestion behavior and health benefits in silver carp surimi. The study found that incorporating ball-milled and irradiated crayfish shell powder into surimi significantly reduced protein digestibility, improved cholesterol-lowering activity, and selectively promoted the release of essential amino acids.
Peptidomics played a crucial role in this research by enabling the identification and quantification of peptides released during simulated digestion. The comprehensive peptide profiling allowed the researchers to uncover bioactive peptides and lipid-regulatory pathways, shedding light on the functional benefits of crayfish shell powder. By providing detailed insights into the digestion process, peptidomics helped link structural changes in surimi to enhanced health benefits, offering valuable information for developing functional foods.
Peptidomics Analysis of Surimi Gel Digests: Peptide Identification and Protein Profile Differences Across Digestive Phases (Chen et al., 2025)
Sample Requirements of Peptidomics Analysis
| Sample Class | Sample Type | Recommended | Minimum |
| Animal Tissue | Normal Tissues (Heart, Liver, Spleen, Lung, Kidney, Brain, Intestine, Stomach, Pancreas, Gallbladder, Testis, Ovary, Breast, Prostate, Thyroid, Adrenal Gland, Lymph, Muscle, Blood Vessel) | 100mg | 50mg |
| Fatty Tissue, Skin, Synovium | 1g | 500mg | |
| Bone, Shell, Eggshell | 1g | 500mg | |
| Cartilage Tissue | 1g | 500mg | |
| Hair | 1g | 500mg | |
| Plant Tissue | Young Tissue (Young Leaves, Petals, Callus Tissue) | 200mg | 100mg |
| Mature Tissue, Stems, Algae, Large Fungi (Mushrooms) | 2g | 1.5g | |
| Bark, Roots, Fruits, Tuberous Roots, Tubers, Root Nodules | 2g | 1.5g | |
| Cells | Primary Cells | 1×10^7 | 5×10^6 |
| Transmissible Cells | 5×10^6 | 3×10^6 | |
| Microorganisms | Bacteria | 300mg | 150mg |
| Fungi | 300mg | 150mg | |
| Liquid Samples | Serum/Plasma (No Low-abundance Enrichment) | 200uL | 50μL |
| Cerebrospinal Fluid, Ascites | 300ul | 150ul | |
| Amniotic Fluid, Milk | 200uL | 50uL | |
| Urine | 20ml | 10ml | |
| Cellular supernatant | 50ml | 25ml |
FAQ for Peptidomics
A peptide is a short chain of amino acids (typically 2 to 50) linked by peptide bonds. Peptides are formed through the degradation or cleavage of proteins via proteolysis, or as part of post-translational modifications (PTMs) that alter proteins after they are synthesized. Peptides can also be synthesized biologically through specific enzyme actions. In the organism, peptides serve a variety of crucial functions, including cell signaling, hormone regulation (e.g., insulin, glucagon), immune responses, and enzyme activity modulation. They can act as neurotransmitters, growth factors, or even defensive molecules (such as antimicrobial peptides), playing essential roles in metabolic regulation, cell communication, and disease resistance.
Peptidomics focuses on the identification and quantification of small peptides (typically 2-50 amino acids), which are often generated through post-translational modifications or protein degradation. In contrast, proteomics studies full-length proteins, typically larger than peptides, to understand their structure, function, and interactions. The primary difference lies in the sample preparation and analytical techniques: proteomics often requires protein digestion into peptides for identification, whereas peptidomics directly analyzes the peptides without the need for prior digestion, offering insights into biologically active peptides that are often missed by proteomics and metabolomics.
Peptidomics is essential for studying endogenous peptides, which play critical roles in regulating various physiological processes such as cell signaling, metabolism, and immune responses. These small peptides often fall between metabolomics and proteomics in size and functionality, making them crucial for understanding complex biological networks. Traditional proteomics and metabolomics often miss these molecules, but peptidomics provides a delicated approach to reveal bioactive peptides that have significant implications in disease mechanisms, biomarker discovery, and therapeutic interventions.
Peptidomics offers several advantages over traditional peptide-based assays, including the ability to profile the entire peptide pool without the need for prior peptide selection or antibody-based enrichment. This non-targeted approach allows for the discovery of novel peptides and unexpected biomarkers that could be missed with traditional methods.
Reference
1. Hellinger, R., Sigurdsson, A., Wu, W. et al. Peptidomics. Nat Rev Methods Primers 3, 25 (2023). https://doi.org/10.1038/s43586-023-00205-2
2. Chen M, Su Y, Xiang A, et al. Leveraging ultra-micro crayfish shell powder to modulate protein digestion and health benefits in silver carp surimi. Food Chem. 2025;488:144900. https://doi.org/10.1016/j.foodchem.2025.144900
