Peptidomics Analysis Services

Applied Biomics provides peptidomics analysis services for the identification and quantification of endogenous peptides in plasma, serum, tissues, cultured cells, and other biological samples. Unlike conventional proteomics, peptidomics analyzes naturally occurring peptides without enzymatic digestion, preserving their native sequences and cleavage sites.

Advantages of Our Peptidomics Services:

• Customized Sample Preparation: Optimize peptide extraction for different sample types
• Comprehensive Peptide Profiling: Identify endogenous peptides in diverse biological samples.
• No Enzymatic Digestion: Preserve native peptide sequences and cleavage sites.
• High-Resolution LC-MS/MS: Accurate peptide identification using Orbitrap mass spectrometry.
• Label-Free Quantification: Compare peptide abundance between experimental groups.
• Bioinformatics Analysis: Peptide identification, quantification, and statistical analysis.

Peptidomics Applications:

• Suitable sample types: All biological samples
• Peptide Biomarker Discovery: Identify disease-associated endogenous peptides.
• Differential Peptide Profiling: Compare peptide abundance between experimental groups.
• Protein Processing and Proteolysis: Study protein cleavage and degradation products.
• Neuropeptide Analysis: Identify peptides involved in neuronal signaling.
• Cancer Research: Discover cancer-associated peptide profiles.
• Drug Discovery: Investigate peptide changes following drug treatment.
• Peptide Hormones and Signaling: Characterize biologically active signaling peptides.

Peptidomics Analysis Workflow

Our peptidomics workflow is designed to recover naturally occurring peptides while minimizing artificial peptide generation and degradation during sample preparation.

• Sample Preparation: Extract endogenous peptides from biological samples.
• Peptide Enrichment & Cleanup: Remove interfering proteins and contaminants.
• NanoLC-MS/MS Analysis: Analyze peptides using high-resolution Orbitrap mass spectrometry.
• Peptide Identification: Identify peptides using no-enzyme database searching.
• Label-Free Quantification: Compare peptide abundance across samples.
• Statistical Analysis (Optional): Determine fold changes, P-values, and differential abundance.
• Biological Interpretation (Optional): Identify precursor proteins and biological significance.

Peptidomics Deliverables

• Peptide Identification Report
  • Identified endogenous peptide sequences
  • Corresponding precursor protein accession numbers and descriptions
  • Peptide molecular masses
  • Peptide-spectrum match confidence metrics
  • Peptide modifications, when included in the analysis

• Quantitative Peptidomics Report
  • Peptide abundance for individual samples
  • Relative peptide abundance ratios between experimental groups
  • Statistical P-values where applicable

Endogenous Peptide Profiling and Quantitative Peptidomics

We offer two major peptidomics study designs:

• A. Endogenous Peptide Identification and Profiling
• B. Comparative Peptidomics With Label-Free Quantification

A. Endogenous Peptide Identification and Profiling

Endogenous peptides are extracted from biological samples without enzymatic digestion, followed by enrichment and high-resolution nanoLC-MS/MS analysis. Peptides and their precursor proteins are identified through no-enzyme database searching.

Figure 1. Representative LC-MS chromatogram showing separation and detection of endogenous peptides.

Figure 2. Representative MS/MS spectrum illustrating endogenous peptide sequence identification.

B. Comparative Peptidomics With Label-Free Quantification

Comparative peptidomics is designed to identify endogenous peptides whose abundance changes between different biological conditions, disease states or drug treatments.