The gut microbiome, a complex ecosystem of trillions of microorganisms residing in the human digestive tract, plays a critical role in human health and disease. While traditional 'omics' methods like metagenomics and metatranscriptomics provide valuable insights into the genetic potential and gene expression of these microbial communities, they often fail to capture the real-time functional activity. This is where metaproteomics comes in, offering a direct window into the actual molecular machinery at work. Creative Biolabs' comprehensive metaproteomics service provides an in-depth, functional characterization of the gut microbiome, enabling researchers and clinicians to move beyond "who is there?" to "what are they doing?"
Overview
Metaproteomics is the large-scale study of the entire protein complement, or proteome, of a microbial community at a specific point in time. It provides direct, quantitative information about the proteins that are being actively expressed and their functional roles. This is crucial because a microbe's genetic potential (metagenomics) doesn't always reflect its actual function, as gene expression is dynamic and can be influenced by a myriad of environmental factors. By analyzing the proteins, we can understand the metabolic processes, enzymatic activities, and host-microbe interactions that are truly happening within the gut.
Accelerate Gut Microbiota Research with Targeted Metaproteomics Services
We offer a flexible and comprehensive suite of metaproteomics services to meet diverse research needs.
Workflow: From Sample to Report
Service Details
Deliverables
Turnaround Time
Services
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Discovery Metaproteomics: A non-targeted approach to identify and quantify as many proteins as possible from your samples. This is ideal for initial exploration, biomarker discovery, and hypothesis generation.
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Targeted Metaproteomics (SRM/PRM): A highly sensitive and reproducible targeted approach to precisely quantify a predefined set of proteins of interest. Perfect for validating biomarkers or monitoring specific protein changes in a large cohort study.
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Integrated Multi-Omics Analysis: We offer the seamless integration of metaproteomics data with other 'omics' data, such as metagenomics, metatranscriptomics, and metabolomics. This holistic approach provides a more complete picture of the microbiome's structure and function.
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Post-Translational Modification (PTM) Analysis: Go beyond simple protein abundance to understand how proteins are functionally regulated. We offer specialized analysis for PTMs like phosphorylation, acetylation, and glycosylation, which are critical for host-microbe signaling.
Sample Information
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Sample Type: Primarily human or animal fecal samples. Other sample types, such as intestinal biopsies, luminal aspirates, or environmental samples, can also be analyzed.
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Sample Collection: Fecal samples should be collected into a sterile container and immediately frozen at -80°C to preserve proteins.
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Minimum Sample Amount: We recommend a minimum of 2-5 grams of fresh fecal material per sample. It is suggested to provide backup samples.
Deliverables
Upon completion of the project, you will receive a comprehensive report that includes:
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A detailed project summary and methodology.
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Raw Mass Spectrometry Data (.raw files).
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Identified Peptide and Protein Lists: Including peptide sequences, protein accession numbers, and confidence scores.
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Protein Abundance Data: Quantitative data for all identified proteins.
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Taxonomic and Functional Annotation Files: Mapping proteins to species and metabolic pathways.
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Statistical Analysis Results: Differential protein lists, heatmaps, volcano plots, and principal component analysis (PCA) plots.
Turnaround Time
Our standard TAT is 10-12 weeks from sample receipt to delivery of the final report. This time frame may vary depending on the project scope, sample complexity, and required data analysis. Expedited services are available upon request.
Ready to move beyond taxonomic profiling to a true understanding of function? Click here to request a quote and consultation!
Our Competitive Advantages
Deep Expertise
Our team consists of Ph.D.-level scientists with extensive experience in mass spectrometry, gut microbiome research, and bioinformatics.
Cutting-Edge Technology
We use the latest generation of high-resolution mass spectrometers and sophisticated data analysis platforms to ensure the deepest proteome coverage and the most accurate quantification.
Customized Solutions
We don't believe in a one-size-fits-all approach. Every project is unique, and we tailor our services and analyses to meet your specific research needs.
Integrated Multi-Omics
We are one of the few CROs that offer a truly integrated multi-omics platform, providing a holistic understanding of your biological system from a single partner.
Actionable Insights
Our reports go beyond data dumps. We focus on providing clear, biologically meaningful insights that help you advance your research and make informed decisions.
Applications
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Disease Biomarker Discovery: Identifying specific microbial proteins that can serve as early diagnostic or prognostic markers for diseases like Inflammatory Bowel Disease (IBD), obesity, or colorectal cancer.
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Therapeutic Development: Understanding the mechanism of action of probiotics, prebiotics, or live biotherapeutic products by monitoring changes in the gut proteome.
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Nutritional and Dietary Studies: Investigating how specific diets or nutritional interventions alter the functional landscape of the gut microbiome.
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Drug Metabolism and Efficacy: Studying how gut microbes metabolize drugs and how these interactions influence drug efficacy and toxicity.
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Host-Microbe Interaction Research: Elucidating the molecular communication between gut microbes and the host immune system.
The Necessity of Metaproteomics
While metagenomics tells you what can be done, and metatranscriptomics tells you what is being transcribed, only metaproteomics tells you what is actually being done. Gene presence doesn't guarantee gene expression, and RNA levels don't always correlate with protein abundance due to post-transcriptional and post-translational regulation. Metaproteomics closes this knowledge gap, offering a critical layer of information for a complete understanding of the gut microbiome's role in health and disease.
Navigating complex gut microbiome research requires specialized expertise. Partner with our team to leverage our state-of-the-art metaproteomics platform and extensive bioinformatics capabilities. Let's collaborate to translate your project goals into actionable, high-impact results.
Your Partner in Metaproteomics Discovery. Schedule a call with a Metaproteomics Specialist.
Frequently Asked Questions (FAQs)
Why is metaproteomics more challenging than traditional proteomics?
Metaproteomics deals with an extremely complex sample matrix. Fecal samples contain a high diversity of microbial species and a vast dynamic range of protein abundances, from highly expressed housekeeping proteins to low-abundance signaling proteins. There's also significant contamination from host proteins. Our specialized sample preparation and fractionation techniques are designed to overcome these challenges.
Do I need to provide metagenomic data?
While not strictly mandatory, providing corresponding metagenomic data is highly recommended. Using a custom protein database generated from your own metagenome sequencing data significantly improves peptide and protein identification rates, as it is specific to the microbial species present in your samples.
What is the difference between metaproteomics and metatranscriptomics?
Metatranscriptomics analyzes the RNA transcripts (mRNA) in a community, which indicates which genes are being expressed. Metaproteomics analyzes the proteins, which are the final functional products of gene expression. Protein levels often don't directly correlate with mRNA levels, making metaproteomics a more direct measure of function.
How do you handle batch effects in a large study?
We have strict quality control protocols and a robust sample randomization strategy to minimize technical variability and batch effects. For large cohorts, we recommend processing all samples from a single study at the same time and using a standard reference sample to normalize data across runs.
