MtoZ Biolabs utilizes high-resolution LC-MS/MS platform and has launched the shotgun protein identification service which enables rapid and comprehensive identification and analysis of proteomes in complex samples. This service is suitable for profiling the overall protein composition of various biological samples and provides a reliable data foundation for proteomics research.

What Is Shotgun Proteomics?

Shotgun proteomics is a high-throughput protein analysis strategy based on the "digest first, then separate, then identify" workflow, in which complex protein samples are directly digested into peptides and then deeply analyzed through LC-MS/MS. This method does not require prior gel separation and can cover a large number of proteins in a single run, making it suitable for comprehensive characterization of proteins in complex biological systems. The Shotgun strategy can rapidly resolve the protein composition of complex samples and is an important approach for investigating protein expression changes, screening biomarkers, and conducting system-level proteomics research.

Nesvizhskii, A I. Journal of Proteomics, 2010.

Figure 1. Overview of Shotgun Proteomics.

Shotgun Protein Identification Service at MtoZ Biolabs

MtoZ Biolabs uses high-resolution mass spectrometry to provide rapid identification and compositional analysis of proteins in complex samples.

• Identify protein types and peptide information in the sample
• Analyze protein abundance changes and basic structural characteristics
• Identify potential modified proteins and key biological molecules
• Resolve protein expression differences under different treatments or conditions

Our analysis can help comprehensively understand the protein composition of samples, supporting researchers in accurately obtaining key information and advancing subsequent experiments and data interpretation.

Workflow of Shotgun Protein Identification Service

1. Sample Pretreatment

Proteins are reduced, alkylated, and digested to convert complex protein mixtures into peptides suitable for mass spectrometry analysis.

2. Peptide Separation

High-performance liquid chromatography is used to separate peptides in a gradient manner, reducing matrix interference and improving subsequent detection performance.

3. LC-MS/MS Analysis

High-resolution mass spectrometry is used to acquire MS1 and MS2 spectra, obtaining accurate mass and fragment information of peptides.

4. Database Search

Sequence matching is performed based on mass spectrometry data to identify protein IDs, coverage, peptide information, and quantitative results.

5. Data Organization and Quality Control

Identification data are evaluated for quality, and standardized reports and related spectra are generated to ensure reliable and reproducible results.

Why Choose MtoZ Biolabs?

• High-Throughput Analysis: A single analysis can obtain large-scale protein information with high coverage.
• High Sensitivity: Low-abundance proteins can be detected, improving overall identification depth.
• Good Reproducibility: Standardized digestion and quality control procedures ensure stable and reliable results.
• Excellent Quantification Capability: Supports multiple quantification strategies, including label-free and TMT.
• One-Stop Analysis: Covers the entire process from sample preparation and detection to data interpretation, improving project efficiency.

Applications of Shotgun Protein Identification Service

1. Differential Protein Screening

Used to compare protein expression differences under different treatments, disease models, or time points, enabling rapid identification of significantly altered proteins.

2. Biomarker Discovery

Suitable for screening potential biomarkers from tissue, cell, or biofluid samples, providing candidate molecules for subsequent validation.

3. Analysis of Protein Composition in Complex Samples

Capable of comprehensively analyzing the protein composition of complex samples such as tissues, microbial communities, and cell lysates.

4. Recombinant Protein Expression Assessment

Can be used to monitor protein expression, impurity components, and modification status in recombinant systems, supporting quality control.

5. Metabolic Pathway and Functional Annotation 

Based on protein identification results, performs pathway enrichment and functional analysis to help elucidate biological processes.

Deliverables

• Comprehensive Experimental Details
• Materials, Instruments, and Methods
• Protein Identification Results
• Spectral and Chromatographic Images
• Bioinformatics Analysis
• Raw Data Files

FAQ

Q1: What types of samples are suitable?

A1: Suitable samples include protein materials with clear origins that can be fully digested, such as cell lysates, tissue extracts, serum, plasma, purified proteins, and other complex protein mixtures. Low-abundance or high-background samples can achieve improved identification depth through pretreatment. For special sample types, it is recommended to consult in advance for more accurate operational guidance.

Q2: What is the service general workflow?

A2:

Q3: What data formats are provided?

A3: MtoZ Biolabs provides multiple standardized output formats, including:

• Mass spectrometry raw data files (such as .raw platform formats)
• Protein and peptide identification results (Excel/CSV)
• PDF analysis report (including method overview, identification statistics, and key results)
• Image files (mass spectra, matched spectra, QC plots, etc., in PNG/TIFF formats)

If special analytical requirements exist, data formats can be customized according to project specifications.

Q4: How should I prepare my samples?

A4: To ensure optimal identification performance, please prepare samples as follows:

• Sample Purity: Avoid high salt, detergents, glycerol, DTT, and other components that may interfere with enzymatic digestion or mass spectrometric ionization.
• Sample Storage: Store at 4℃ for short-term, and at −80℃ for long-term preservation. Minimize freeze-thaw cycles to prevent protein degradation.
• Sample Shipment: Use low-temperature shipping conditions (ice packs or dry ice) and sealed containers to prevent leakage or contamination.
• Additional Information: Please provide sample type, concentration, buffer system, pretreatment steps, and research objectives to enable selection of the most suitable analytical strategy.

For more information, please refer to Sample Submission Guidelines for Proteomics, Sample Submission Guidelines for Metabolomics.

Start Your Project with MtoZ Biolabs    

Contact us to discuss your experimental design or request a quote. Whether you aim to comprehensively profile protein composition or investigate protein changes under different conditions, MtoZ Biolabs can provide precise and reliable Shotgun protein identification support.