Microorganisms Proteomics Solutions

Microorganisms play a central role in human health (e.g., gut microbiota), industrial production (e.g., biofuel synthesis), and environmental ecosystems (e.g., bioremediation). Proteins serve as the molecular engines driving these microbial activities. Microorganisms proteomics is a key technology that enables comprehensive analysis of microbial proteins (including bacteria, fungi, algae, etc.), revealing their functions, interactions, and environmental response mechanisms. By bridging the gap between genetic potential and actual microbial behavior, this field facilitates breakthroughs in drug development, industrial biotechnology, and environmental sustainability.

 

Microorganisms proteomics provides deep insights into how pathogens influence host protein networks, disrupt immune signaling, and adapt to environmental changes. By leveraging high-resolution mass spectrometry, it enables the identification of key virulence factors, antigenic proteins, and antibiotic resistance-related proteins, supporting the development of novel antimicrobial strategies and precision medicine.

 



Figure 1. Research Areas in Medical Microbiology That Utilize Proteomic Technologies

 

MtoZ Biolabs offers cutting-edge microorganisms proteomics solutions, delivering high-precision protein insights to empower both research and industrial innovation. We provide fully customized end-to-end analysis, covering:

1. Discovery Proteomics: Utilizing DIA (Data-Independent Acquisition) mass spectrometry, we quantify over 9,000 proteins in a single experiment, capturing low-abundance targets and providing a comprehensive proteomic landscape.
2. Targeted Proteomics: Using PRM (Parallel Reaction Monitoring) technology, we achieve precise quantification of 150+ target proteins, ideal for biomarker validation or core pathway monitoring.
3. Functional Annotation and Network Analysis: Integrating KEGG, GO databases, and interaction networks, we transform raw data into meaningful biological insights.

 

From single bacterial strains to complex microbial communities (metaproteomics), and from pathogen-host interactions to industrial fermentation monitoring, our services cover the full spectrum of microbial research.

 

Analysis Workflow

1. Sample Preparation and Collection

Microbial communities are collected from environmental samples such as water, soil, and gut microbiota. Depending on the sample type, two different processing methods can be applied:

• Cell fractionation and concentration: Techniques such as membrane filtration and ultrafiltration are used to isolate microbial cells, improving protein extraction efficiency.
• Direct separation from the environmental matrix: Some special samples allow direct protein extraction without prior cell isolation.

 

2. Community Proteomic Extraction

After separation, proteins are extracted using methods such as lysis buffer treatment, ultrasonication, or French press lysis. The extracted proteins may be labeled for quantitative proteomics analysis.

 

3. Protein Separation

Extracted proteins are separated to improve identification accuracy and resolution. This step can involve:

• One-dimensional (1-DE) and two-dimensional gel electrophoresis (2-DE): Proteins are separated, and specific spots of interest are excised for trypsin digestion.
• Multidimensional liquid chromatography: This technique, combined with 2-DE or high-performance liquid chromatography (HPLC), enhances the separation of complex samples.

 

4. Mass Spectrometry Analysis

The digested protein peptides are analyzed using various types of mass spectrometry (MS, MS/MS). This step generates a large amount of MS/MS data, which is then used for protein identification.

 

5. Protein Identification and Interpretation

Mass spectrometry data is used for protein identification through the following methods:

• Peptide mass fingerprinting (PMF): Matches peptide mass patterns to known databases.
• Database searches with MS/MS data: Identifies peptides by comparing MS/MS spectra with protein sequence databases.
• De novo sequencing: Determines peptide sequences without relying on a reference database, using sequence-tag searches to infer novel protein sequences, which is particularly useful for unknown microbial proteins.

 



Wang, DZ. et al. Int J Mol Sci. 2016.

Figure 2. Typical Workflow for Microorganisms Proteomics Analysis

 

Service Advantages

• Unparalleled Accuracy: Data reproducibility reaches 99%, with a dynamic range spanning six orders of magnitude, ensuring highly reliable results.
• High-Throughput Efficiency: Analyze thousands of proteins per experiment, optimizing time and cost.
• Broad Compatibility: Supports diverse microbial types, including clinical isolates, engineered strains, and environmental samples.
• Expert Support: A team of PhD-level scientists provides comprehensive assistance in experimental design, data analysis, and research translation.
• Multi-Omics Integration: Seamlessly combines genomics, metabolomics, and proteomics for multidimensional research perspectives.

 

Case Study

1. Next-Generation Proteomics for Quantitative Jumbophage-Bacteria Interaction Mapping

This study utilized co-fractionation mass spectrometry (CF-MS) for high-throughput analysis of the interactions between Pseudomonas aeruginosa and two jumbophages (ϕKZ and ϕPA3), overcoming the limitations of affinity purification mass spectrometry (AP-MS) in scalability and biological authenticity. The study identified over 6,000 unique host-phage interactions, covering more than 50% of each phage's proteome. The results revealed interactions between KZ-like phage proteins and the host ribosome, as well as novel phage protein complexes, including an RNA polymerase complex in ϕPA3. Comparative interactome analysis across phages suggested that the KZ-like phage family shares conserved predation mechanisms. Additionally, the researchers developed PhageMAP, an online database for network querying, visualization, and interaction prediction, facilitating large-scale studies of host-pathogen interactomes.

 



Fossati, A. et al. Nat Commun. 2023.

Figure 3. High-Throughput Interaction Proteomics for Deep Host–Pathogen Interaction Mapping

 

2.MS-Based Thermal Stability Profiling in Bacteria: Probing Protein State in vivo

This study adapted MS-based thermal stability profiling to investigate the thermostability of Escherichia coli proteins in vivo, providing insights into bacterial protein states and antimicrobial mechanisms. The E. coli proteome exhibited higher thermostability than human cells, with a gradient from high stability at the cell surface to lower stability in the cytoplasm. While protein complexes within the same compartment melted similarly, those spanning multiple compartments exhibited location-dependent melting patterns. By analyzing the E. coli meltome and proteome across different growth phases, researchers observed metabolic changes and significant physiological shifts in TolC-deficient cells, including altered thermostability of interaction partners, signaling cascades, and periplasmic quality control. Combining in vitro and in vivo MS-based thermal stability profiling, they identified antimicrobial drug targets and their downstream effects. This study demonstrates that MS-based thermal stability profiling is a powerful tool for probing protein complex architecture, metabolic pathways, and intracellular drug interactions in bacteria.

 



Mateus, A. et al. Mol Syst Biol. 2018.

Figure 4. MS-based thermal stability profiling in Escherichia coli

 

Applications

1. Clinical and Pharmaceutical Research

• Unraveling antibiotic resistance mechanisms in pathogens like Pseudomonas aeruginosa and Mycobacterium tuberculosis.
• Identifying virulence factors to accelerate anti-infective drug target discovery.

 

2. Industrial Biotechnology

• Optimizing metabolic pathways in enzyme-producing strains to enhance biofuel and enzyme production.
• Real-time monitoring of fermentation protein quality to ensure process stability.

 

3. Environmental Microbiology

• Investigating adaptation mechanisms in extremophiles (e.g., thermophiles, halophiles).
• Analyzing microbial functional activity in wastewater treatment and soil remediation.

 

Deliverables

1. Raw Data & Mass Spectrometry Profiles: Fully transparent and publication-ready.

2. Quantitative Analysis Reports: Protein abundance, fold-change differences (p-value ≤ 0.05), and statistical significance.

3. Functional Annotation Maps: Enrichment of metabolic pathways, protein interaction networks, and complex analyses.

 

Whether you are exploring pathogenic mechanisms, optimizing industrial strains, or decoding environmental microbial communities, MtoZ Biolabs' microorganisms proteomics solutions provide precise data and deep insights to keep you ahead of the curve. Contact us today to customize your research plan and unlock the protein code of the microbial world!