Shotgun Proteomics Service

Shotgun proteomics is a bottom-up proteomics approach that involves random enzymatic digestion of proteins into peptides, followed by liquid chromatography (LC) and high-resolution mass spectrometry (MS) for comprehensive analysis of proteins in complex biological samples. Its “shotgun” strategy eliminates the need for protein separation, enabling the identification and quantification of thousands of proteins in a single experiment.

 

MtoZ Biolabs offers precise and reliable shotgun proteomics service utilizing advanced mass spectrometry platforms such as Orbitrap Fusion Lumos and Q Exactive HF, along with nanoLC systems. Our service combines cutting-edge technology with optimized workflows to support both basic research and applied development in proteomics.

 

Analysis Workflow

MtoZ Biolabs provides efficient and reliable shotgun proteomics service through standardized protocols and optimized workflows. The main steps include:

• Sample Preparation: Extraction and quantification of proteins from cells, tissues, or biological fluids. We ensure high-quality samples for enzymatic digestion and subsequent analysis.
• Enzymatic Digestion: Proteins are randomly digested into peptides using enzymes like trypsin, ensuring a uniform sample for mass spectrometry analysis.
• Liquid Chromatography Separation: Peptides are separated using a nanoLC system for thorough analysis of complex samples.
• Mass Spectrometry Detection: High-resolution mass spectrometers (such as Orbitrap Fusion Lumos) detect peptide masses and fragmentation, yielding accurate protein identification and quantification.
• Data Analysis: Using optimized databases and algorithms, we provide in-depth analysis of the data, achieving a comprehensive characterization of proteins in the sample.

 

Zhu, Y. F. et al. Karolinska Inst. 2018.

 

Service Advantages

1. Advanced Analysis Platform: MtoZ Biolabs established an advanced shotgun proteomics platform, guaranteeing reliable, fast, and highly accurate analysis service.

2. One-Time-Charge: Our pricing is transparent, no hidden fees or additional costs.

3. High-Data-Quality: Deep data coverage with strict data quality control. AI-powered bioinformatics platform integrate all proteomics data, providing clients with a comprehensive data report.

4. Broad Sample Compatibility: Our platform accommodates various biological samples—from purified proteins to complex matrices like cell lysates, tissues, and bodily fluids—to meet diverse research needs.

5. Customized Service: Tailored to the specific research needs of our clients, we offer flexible experimental design and personalized data analysis to ensure the achievement of research goals to the fullest extent.

 

Sample Submission Suggestions

To optimize results from our shotgun proteomics service we recommend consulting our technical team for specific guidance on sample preparation. General recommendations are as follows:

• Low-complexity samples: Gel spots or bands, approximately 1-2 cm in length.
• Medium-complexity samples: Protein mixtures, including column-purified samples.
• Moderate-to-high complexity samples: Protein mixtures such as IP-derived samples, secreted proteomes, or subcellular organelles (e.g., mitochondria, endoplasmic reticulum, lysosomes).
• High-complexity samples: Whole cell lysates, tissues.

 

For more specific sample submission requirements, please consult our technical team.

 

Applications

Shotgun proteomics service is widely used in life science research to explore biological systems and mechanisms. Key applications include:

• Disease Biomarker Research: Screening and validating biomarkers for disease diagnosis.
• Drug Development and Target Identification: Investigating drug mechanisms and identifying potential targets.
• Post-translational Modification Research: Studying the effects of modifications like phosphorylation and acetylation on protein function.
• Analysis of Biological Networks and Signaling Pathways: Uncovering functional relationships between proteins.
• Basic Life Sciences Research: Investigating cellular metabolism and biological processes at the molecular level.

 

Case Study

Case1

A study utilizing shotgun proteomics identified microbial molecular phenotypes by comparing protein expression levels. The research revealed specific molecular features of microbes under various conditions, providing valuable insights into microbial behavior and adaptation.

 



Gouveia, D. et al. Environ. Microbiol. 2020.

 

Case 2

In a comprehensive shotgun proteomics study of 11 seafood spoilage-related bacteria, 3,817 proteins were identified, with 4,455 peptide-spectrum matches and 4,299 peptides. Further analysis identified 773 peptides as virulence factors associated with bacterial pathogenicity and 14 peptides as biomarkers distinguishing bacterial species. These findings, published in [Author et al., Year], offer a deeper understanding of the molecular mechanisms behind seafood spoilage and its virulence characteristics.

 

Abril, A. G. et al. Food Chem. 2024.

 

FAQ

Q1: How does shotgun proteomics address protein abundance variation in samples?
In complex biological samples, protein abundance can vary significantly. To address this, MtoZ Biolabs employs optimized digestion methods and advanced nanoLC systems to effectively separate and detect low-abundance proteins in a high-abundance background. Our high-resolution mass spectrometers (e.g., Orbitrap Fusion Lumos) offer a broad dynamic range and excellent sensitivity for detecting low-abundance proteins. Additionally, we use enrichment strategies (e.g., phosphorylation or glycosylation enrichment) to further enhance the detection of specific proteins or modifications.

 

Q2: What specific information does the data analysis provide?
Our shotgun proteomics service offers protein identification and quantification, along with analysis of post-translational modifications (e.g., phosphorylation, acetylation) to reveal protein function and regulation. Clients receive detailed protein lists, peptide matching data, and quantitative results, with the option for additional functional enrichment and signaling pathway analysis. MtoZ Biolabs' personalized data analysis services enable clients to uncover valuable scientific insights.

 

MtoZ Biolabs, an integrated Chromatography and Mass Spectrometry (MS) Services Provider, provides advanced proteomics, metabolomics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption. Free project evaluation, welcome to learn more details!