Mass Spectrometry (MS) Service for Ribosomal Proteomics
Are you presently grappling with difficulties in comprehending the intricate dynamics of protein synthesis, pinpointing new therapeutic targets, or unraveling the mechanisms underlying diseases at the translational stage? Our mass spectrometry (MS) ribosomal proteomic service helps you gain unparalleled insights into active translation and ribosomal composition through advanced MS. We bridge the critical gap between mRNA and protein expression, providing a direct snapshot of cellular protein production.
Overview of MS Ribosomal Proteomic Service
Ribosomes are the central machinery for protein synthesis, translating genetic information from mRNA into functional proteins. Beyond their canonical role, ribosomal proteins and their post-translational modifications are increasingly recognized as crucial regulators of cellular processes and disease progression. MS based ribosomal proteomics offers an unparalleled approach to comprehensively characterize these intricate complexes, providing direct evidence of active translation and uncovering subtle yet significant alterations in ribosomal composition and modification states. This direct analysis bridges the critical gap between gene expression and protein function, revealing regulatory layers undetectable by transcriptomics alone and thus advancing our understanding of biological systems and disease etiology.
Fig.1 Workflow in a bottom-up proteomics experiment.1
Key Procedures
Our MS based ribosomal proteomic service follows a meticulously designed workflow, ensuring the provision of top-notch, actionable data.
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Sample Preparation & Ribosome Isolation
Cells or tissues are carefully lysed, followed by optimized sucrose cushion ultracentrifugation or polysome profiling to enrich for ribosomal fractions. This critical step ensures the isolation of intact, functionally active ribosomes, minimizing contamination from non-ribosomal proteins. -
Protein Extraction & Digestion
Proteins are extracted from the purified ribosomal fractions. These proteins undergo a rigorous digestion process, typically using trypsin, to generate peptides suitable for MS analysis.
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LC-MS/MS Data Acquisition
The peptide mixture is separated by high-resolution liquid chromatography (LC) and then introduced into a state-of-the-art mass spectrometer, such as an Orbitrap-based system. Data-dependent acquisition (DDA) or data-independent acquisition (DIA) methods are employed to identify and quantify thousands of ribosomal proteins and associated factors with high sensitivity and accuracy.
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Bioinformatic Analysis & Data Processing
Raw MS data undergo extensive bioinformatic processing. This includes peptide-spectrum matching, protein inference, relative or absolute quantification, and statistical analysis to identify differentially expressed ribosomal proteins or PTMs between experimental groups.
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Functional Annotation & Pathway AnalysisThe identified and quantified ribosomal proteins are subjected to comprehensive functional annotation, including GO term enrichment, KEGG pathway analysis, and protein-protein interaction network mapping. This provides biological context and helps uncover the implications of changes in ribosomal composition.
Applications
- Translational Control Studies
Elucidate how cellular conditions, stress, or therapeutic interventions influence mRNA translation efficiency by analyzing changes in ribosomal composition and modification.
- Disease Mechanism Elucidation
Identify ribosomal protein dysregulation or altered PTMs associated with various pathologies, including cancer, neurological disorders, and metabolic diseases, providing insights into disease etiology.
- Biomarker Discovery
Discover novel diagnostic or prognostic biomarkers by identifying unique ribosomal protein signatures in patient samples, offering a direct measure of active protein synthesis related to disease state.
- Drug Target Identification
Pinpoint ribosomal proteins or associated factors as potential therapeutic targets for small molecules or biologics aimed at modulating protein synthesis pathways.
- Mechanistic Toxicology
Understand the ribosomal response to drug exposure or environmental toxins, providing insights into potential translational impacts and adverse effects.
- Synthetic Biology & Bioprocessing
Optimize protein production in engineered biological systems by monitoring ribosomal efficiency and composition, crucial for biopharmaceutical manufacturing.
Pivotal Strengths
Creative Biolabs stands at the forefront of MS ribosomal proteomic services, offering unparalleled expertise and state-of-the-art technology. Our dedicated team of proteomics specialists ensures high data quality, comprehensive analysis, and insightful interpretations tailored to your specific research questions. We are committed to accelerating your discoveries by providing reliable, high-resolution insights into the intricate world of ribosomal biology. Our rigorous quality control measures, optimized workflows, and advanced bioinformatics capabilities position Creative Biolabs as your trusted partner in translational research.
FAQs
Q: What types of samples are suitable for your MS ribosomal proteomic service?
A: We can process a wide range of biological samples, including cell cultures and various tissue types. Our team will work with you during the consultation phase to ensure your samples meet the quality and quantity requirements for optimal results.
Q: How does this service provide a more accurate picture compared to transcriptomics?
A: While transcriptomics measures mRNA levels, it doesn't directly indicate which proteins are actively being translated or the functional state of the ribosomes. Our MS ribosomal proteomic service directly analyzes the proteins constituting the ribosomes and those actively engaged in translation, offering a real-time snapshot of protein synthesis that closely correlates with cellular phenotypes. This provides a crucial layer of regulatory insight beyond mRNA abundance.
Q: Can your service identify post-translational modifications (PTMs) on ribosomal proteins?
A: Absolutely. Our advanced MS platforms are highly capable of detecting and quantifying various post-translational modifications on ribosomal proteins, such as phosphorylation, acetylation, and methylation. Understanding these PTMs is critical for unraveling the regulatory mechanisms that control ribosomal function and cellular protein output.
Q: How does Creative Biolabs ensure the quality and reproducibility of its ribosomal proteomics data?
A: Creative Biolabs adheres to stringent quality control protocols at every stage, from sample preparation and ribosome isolation to LC-MS/MS data acquisition and bioinformatics analysis. We utilize high-resolution mass spectrometers, optimized standardized workflows, and rigorous data validation methods.
Related Services
To further support your research into protein synthesis and function, Creative Biolabs offers a suite of complementary services:
For a comprehensive analysis of global protein expression changes beyond ribosomal components.
Delve deeper into specific PTMs on any protein of interest, including phosphorylation, ubiquitination, and glycosylation.
Uncover novel protein complexes and interaction networks that regulate cellular processes, including ribosomal assembly and function.
Creative Biolabs is dedicated to empowering your research with cutting-edge MS ribosomal proteomic services. By providing direct, high-resolution insights into the translational landscape, we help you overcome critical bottlenecks in understanding disease mechanisms, identifying biomarkers, and accelerating drug discovery. Partner with Creative Biolabs to unlock the full potential of your proteomic investigations.
Reference
- Dupree, Emmalyn J., et al. "A critical review of bottom-up proteomics: the good, the bad, and the future of this field." Proteomes 8.3 (2020): 14. DOI: 10.3390/proteomes8030014. Distributed under Open Access license CC BY 4.0, without modification.
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