Shotgun Peptidomics Analysis Service

Shotgun peptidomics analysis is a widely used untargeted approach in peptidomics research, aimed at comprehensive identification of peptides in complex biological samples. Its basic principle involves enzymatic digestion of peptides, liquid chromatography (LC) separation, and high-resolution mass spectrometry (MS) detection, which comprehensively captures peptide information from the sample. Unlike traditional targeted analysis methods, the shotgun approach does not rely on pre-designed targets but instead performs a broad scan of all peptides in the sample, providing high-throughput peptide characterization data.

 

The shotgun peptidomics analysis service is extensively applied in fields such as cell biology, metabolomics, drug development, and disease research. It is particularly suitable for the identification of unknown target peptides, peptoid function studies, and biomarker screening. Through this service, researchers can quickly obtain broad peptide data present in the sample, providing crucial support for subsequent functional studies, differential analysis, and exploration of biological mechanisms.

 

Services at MtoZ Biolabs

Based on a high-resolution mass spectrometry platform, MtoZ Biolabs offers the shotgun peptidomics analysis service focusing on comprehensive peptide analysis from complex biological samples. This service involves peptide digestion, liquid chromatography for peptide separation, and mass spectrometry for high-sensitivity detection and quantitative analysis. The results provide data on peptide mass, abundance, and its matching information with known databases. Clients will receive high-throughput, unbiased peptide spectrum data, supporting protein expression profiles, differential analysis, and functional studies. This service is suitable for applications such as unknown target identification, functional peptide screening, and biomarker discovery.

 

Analysis Workflow

1. Sample Preparation and Protein Extraction

Total proteins are extracted from the sample to ensure purity and quality, while removing interfering substances to provide a reliable foundation for subsequent analysis.

 

2. Protein Digestion and Peptide Generation

Proteins are digested using enzymes to break them down into peptides for further analysis.

 

3. Peptide Separation and LC-MS Analysis

Peptides are separated through liquid chromatography (LC) and analyzed using high-resolution mass spectrometry platforms for precise qualitative and quantitative analysis.

 

4. Data Processing and Peptide Identification

Professional software is used for data processing, including peptide mass and abundance analysis. Known databases are used to match and identify target peptides.

 

5. Result Interpretation and Report Output

Detailed quantitative data and peptide identification results are provided, along with functional annotations and statistical analysis, to help clients understand the role of peptides in biological processes.

 



Nesvizhskii, A I. Nature Methods, 2014.

Figure 1. The Analysis Workflow of Shotgun Peptidomics.

 

Sample Submission Suggestions

1. Sample Types

Supports various biological sample types, including serum, plasma, tissue homogenates, cell lysates, etc. Sufficient sample volume should be provided, and contamination should be minimized to ensure accurate analysis.

 

2. Sample Storage and Transport

Samples should be stored at low temperatures (-80°C) and transported using dry ice to ensure the samples do not degrade during transport. Prior to transport, centrifugation should be performed to remove particulate impurities.

 

3. Sample Information

Please provide detailed background information on the sample, including its source, handling method, and the presence of any exogenous contamination, to optimize the analysis process and ensure the accuracy of the results.

 

Service Advantages

1. High-Throughput Analysis

This service utilizes high-resolution mass spectrometry platforms to support large-scale peptide analysis, enabling rapid acquisition of comprehensive peptidomics data suitable for high-throughput research needs.

 

2. Comprehensive Coverage

Using the shotgun method, this service performs unbiased analysis of peptide samples, capable of detecting all peptides from low to high abundance, providing full support for subsequent research.

 

3. Flexible Data Processing

Advanced bioinformatics support is provided to efficiently analyze and quantify peptide data, helping clients extract valuable information from large datasets and deliver precise results.

 

4. Customized Services

Based on the client’s research requirements and sample characteristics, MtoZ Biolabs offers personalized analysis plans to meet the diverse needs across various research fields.

 

Applications

1. Protein Function Study

The shotgun peptidomics analysis service can be used to study the functional regions and mechanisms of proteins by analyzing peptide variations under different conditions, revealing the biological functions of proteins.

 

2. Biomarker Discovery

By performing peptidomics analysis on biological samples such as blood, urine, and tissues, potential disease biomarkers are discovered, providing support for early diagnosis and therapeutic evaluation.

 

3. Signal Transduction and Metabolic Pathway Research

This service can be applied to explore key peptides involved in intracellular signal transduction pathways and metabolic processes, helping to decipher cellular function regulation and changes in physiological states.

 

4. Food and Nutritional Analysis

In food science, it is used to detect protein hydrolysis products and peptide composition in food, aiding in the assessment of nutritional content and bioactivity.

 

FAQ

Q1: How Does Shotgun Peptidomics Analysis Ensure the Detection of Low-Abundance Peptides?

A1: The shotgun peptidomics approach combines high-resolution mass spectrometry with multiple analyses, enabling effective detection of low-abundance peptides in complex samples. By optimizing sample preparation and data acquisition workflows, we maximize peptide capture from the sample and provide enhanced detection sensitivity.

 

Q2: Can Comparative Analysis Be Performed Across Multiple Samples?

A2: Yes, the shotgun peptidomics approach supports comparisons across multiple samples, making it suitable for quantitative analysis of peptides under different experimental groups, time points, or treatment conditions. Such comparative analysis helps reveal expression differences and functional changes in peptides under varying conditions.

 

Q3: Can Shotgun Peptidomics Analysis Be Used to Study Post-Translationally Modified Peptides?

A3: Shotgun peptidomics analysis can detect peptides with post-translational modifications (PTMs), including phosphorylation, acetylation, and glycosylation. We can employ specific enrichment strategies for modified peptides to enhance detection sensitivity and ensure accurate quantification of these peptides.

 

Deliverables

1. Comprehensive Experimental Details

2. Materials, Instruments, and Methods

3. Data Analysis, Preprocessing, and Estimation

4. Bioinformatics Analysis

5. Raw Data Files