Quantitative phosphoproteomics service is designed to systematically and accurately quantify protein phosphorylation across the proteome using high-resolution mass spectrometry. Since its initial recognition in the 1950s through kinase research, phosphorylation has been extensively studied—particularly after the development of phosphopeptide enrichment methods and high-resolution tandem MS in the 1990s. As a reversible post-translational modification, phosphorylation regulates protein function, localization, and stability, serving as a pivotal mechanism in numerous cellular signaling pathways.
Unlike conventional proteomics, which reflects overall protein abundance, quantitative phosphoproteomics captures dynamic and site-specific phosphorylation changes. This enables researchers to decipher regulatory mechanisms underlying drug response, immune activation, and metabolic adaptation in both physiological and pathological contexts.
To support such in-depth investigations, MtoZ Biolabs offers a specialized quantitative phosphoproteomics service that combines advanced mass spectrometry platforms, optimized phosphopeptide enrichment techniques, and comprehensive bioinformatics analysis. Our service is tailored to deliver high-confidence, reproducible phosphoproteomic data for a broad range of life science applications.
Phosphorylation: A Dynamic Regulator of Cellular States
Phosphorylation is a reversible biochemical process in which a phosphate group is covalently attached to serine, threonine, or tyrosine residues by protein kinases and removed by phosphatases. This modification enables rapid and reversible regulation of:
- Enzymatic activity (e.g., AKT, CDK1)
- Subcellular localization (e.g., STAT1 translocation)
- Protein–protein interactions
- Signal propagation in pathways like MAPK, PI3K-AKT, JAK-STAT)
In contrast to relatively stable PTMs like methylation, phosphorylation is highly sensitive to external stimuli—including stress, nutrient signals, and growth factors. Multiple phosphorylation sites on a single protein can function combinatorially, integrating diverse upstream signals or enabling hierarchical regulation. These features make phosphorylation particularly suited for decoding context-dependent cellular behavior.
Furthermore, phosphorylation frequently interacts with other PTMs, such as ubiquitination and acetylation, forming an interconnected regulatory network. This crosstalk enhances the complexity of signaling control and places phosphorylation at the center of systems biology and disease mechanism research.
Quantitative Phosphoproteomics Service Workflow at MtoZ Biolabs
MtoZ Biolabs provides a comprehensive phosphoproteomics workflow, integrating optimized sample processing, enrichment, quantification, and in-depth data analysis. Each step is designed to ensure high sensitivity, site-level accuracy, and reproducibility.
1. Sample Preparation and Digestion
Samples—including tissues, cells, plasma, or microbial lysates—are processed with phosphatase inhibitors to preserve phosphorylation states. Proteins are digested using trypsin and Lys-C, generating peptides for downstream analysis. Extraction protocols are adapted to retain labile modifications while minimizing variability.
2. Phosphopeptide Enrichment
(1) IMAC and TiO₂: Enrich global phosphopeptides (pSer/pThr)
(2) Anti-pTyr antibodies: Capture rare tyrosine-phosphorylated peptides
(3) Sequential workflows: Applied for low-input or complex matrices
We routinely combine multiple enrichment strategies to ensure broad phosphosite coverage, particularly in signaling studies where tyrosine phosphorylation events are crucial but low in abundance. Additionally, we optimize binding/elution parameters to balance enrichment specificity with phosphopeptide yield.
3. Quantification Strategies for Phosphoproteomics
(1) Labeling-based analysis for quantitative phosphoproteomics (TMT/iTRAQ) for high-throughput, multiplexed studies
(2) DIA-based phosphoproteomics services for unbiased, reproducible quantification with minimal missing data
Each strategy is selected to align with study goals—mechanism elucidation, time-course tracking, or cohort comparison. We also support hybrid designs combining DDA and DIA for reference library generation and comprehensive quantification.
4. LC-MS/MS Acquisition
Samples are analyzed using Orbitrap platforms (Exploris 480, Q Exactive HF-X). Acquisition settings are tuned to optimize phosphopeptide identification, localization, and quantitative accuracy. NanoLC gradients are adapted for sample complexity, ensuring maximal peptide separation and phosphosite detection depth. QC injections and replicate analyses are conducted to assess technical reproducibility.
5. Bioinformatics Analysis and Reporting
Data processing includes:
(1) Phosphosite quantification and normalization;
(2) Kinase–substrate network inference;
(3) Pathway and GO enrichment (KEGG, Reactome);
(4) Statistical testing (fold change, p-values, FDR);
(5) Visual outputs: heatmaps, volcano plots, kinase maps.
We deliver interactive data formats (Excel, PDF, Cytoscape-compatible) and support multi-omics integration upon request, ensuring flexible usability for diverse research pipelines. Optional features include protein interaction maps, co-modification overlays, and temporal phospho-pattern clustering.
Applications of Quantitative Phosphoproteomics
Quantitative phosphoproteomics provides unique insight into the functional regulatory state of cells and tissues by capturing dynamic, site-specific phosphorylation events. Its applications span multiple research fields and disease models:
1. Oncology
Profile phosphorylation changes in key oncogenic pathways (e.g., EGFR, AKT, BRAF) to investigate drug resistance, tumor heterogeneity, and signaling rewiring. Phosphosite-level analysis enables stratification of tumor subtypes and identification of actionable therapeutic targets, offering greater predictive value than mRNA or total protein expression.
2. Neuroscience
Characterize phospho-regulation of neural proteins involved in neurodegeneration (e.g., Tau, TDP-43), synaptic plasticity, circadian rhythms, and neuroinflammation. Phosphoproteomics supports early-stage detection of neurological alterations and reveals molecular underpinnings of cognitive and psychiatric disorders.
3. Immunology
Track phosphorylation dynamics in immune signaling—such as T-cell activation, cytokine response, or innate immune pathways—using in vivo or ex vivo samples. Integration with phospho-flow or transcriptomic data enables detailed immunophenotyping and informs studies on vaccine response, checkpoint inhibition, and autoimmunity.
4. Metabolic Research
Analyze phosphorylation states of metabolic regulators (e.g., AMPK, mTOR, IRS1) under fasting, obesity, or pharmacological treatment. Patterns of phospho-regulation provide insights into energy homeostasis, insulin signaling, lipid metabolism, and mitochondrial adaptation.
5. Pharmacology
Evaluate phosphoproteome changes upon drug exposure to elucidate mechanism of action, adaptive feedback, or off-target effects. Phosphoproteomic profiling supports compound prioritization, toxicity screening, and combination strategy design. When combined with chemical proteomics, it facilitates identification of druggable nodes in perturbed signaling networks.
Modular Phosphoproteomics Solutions at MtoZ Biolabs
Recognizing the diversity of research objectives in cell signaling and disease modeling, MtoZ Biolabs offers modular phosphoproteomics solutions that flexibly integrate with various experimental designs. Each module is built to address specific scientific questions while maintaining compatibility with high-resolution mass spectrometry and advanced data analytics.
1. Global Discovery Module
Facilitates broad-spectrum identification of phosphorylation sites under different biological conditions using high-coverage acquisition strategies. Well-suited for hypothesis generation, disease-control comparisons, and early-stage target discovery.
2. Quantitative Profiling Module
Enables robust site-level quantification across sample cohorts using label-free DIA or multiplexed designs. Supports biomarker validation, treatment monitoring, and cohort-based differential analysis with high reproducibility.
3. Regulatory Pathway Module
Combines phosphosite pattern mining with motif and kinase prediction analysis to infer upstream regulatory signals. Ideal for uncovering pathway-level changes and mapping kinase-substrate interactions in complex systems.
4. Dynamic Response Module
Captures temporal or dose-dependent phosphorylation changes through serial sampling and data-driven clustering. Commonly applied in drug response studies, stress signaling, and kinetic modeling of pathway feedback.
5. Targeted Validation Module
Delivers sensitive, high-confidence quantification of selected phosphosites using targeted MS techniques such as PRM. Supports biomarker refinement, clinical assay development, and translational research initiatives.
Each module can operate independently or be integrated into a customized pipeline, allowing researchers to build scalable phosphoproteomic strategies suited to exploratory or translational studies.
Sample Submission Suggestion for Phosphoproteomic Analysis
Avoid SDS, high-salt, or lipid-rich buffers. For rare, FFPE, or low-input samples, we provide specialized extraction and desalting protocols to ensure LC-MS/MS compatibility. Clients are welcome to consult our technical team in advance for specific recommendations on sample pooling, batching, or pre-treatment strategies.
Why Choose MtoZ Biolabs for Phosphoproteomics Services?
1. Advanced Analysis Platform
We operate state-of-the-art mass spectrometry systems, including Orbitrap Exploris 480 and Q Exactive HF-X, coupled with optimized phosphopeptide enrichment strategies. Whether for discovery research or clinical validation, our platform ensures deep coverage and high localization confidence.
2. Flexible Quantification Options
We support a range of quantification approaches—TMT, iTRAQ, DIA, and PRM—tailored to diverse study types, from large-cohort biomarker screening to targeted site validation.
3. High-Data-Quality
We deliver high-depth phosphoproteomic coverage with rigorous data quality control. Our AI-powered bioinformatics platform integrates multi-dimensional datasets, providing clients with insightful, publication-ready reports.
4. Scientific Expertise
Led by a team with extensive experience in oncology, immunology, metabolism, and drug development, MtoZ Biolabs supports cutting-edge translational research and industry innovation.
5. One-Time-Charge
Our pricing model is completely transparent — no hidden fees or unexpected costs. Each project is defined by a clear scope and supported by regular milestone updates.
What Could Be Included in the Report?
- Experimental setup documentation, sample metadata, and buffer compatibility
- Instrument settings, calibration records, and run-level QC diagnostics
- Raw (.RAW/.mzML) and processed (.csv/.xls) files for all replicates
- Annotated phosphosite tables with abundance values, statistics, and localization confidence
- Kinase motif prediction, upstream network inference, and pathway enrichment (GO, KEGG, Reactome)
- Visualizations: volcano plots, hierarchical clustering, PPI networks, temporal kinetics
- Customizable report formats
Empower Your Research with MtoZ Biolabs’ Quantitative Phosphoproteomics Service
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.
From pathway analysis to clinical target discovery, MtoZ Biolabs’ quantitative phosphoproteomics service delivers the phosphosite-level resolution and interpretability needed to unlock the full complexity of cellular regulation. Whether you’re exploring signaling rewiring in disease or optimizing drug treatment strategies, our high-quality, customizable service platform is built to support your success. We are committed to providing data you can trust for actionable insights.
Contact MtoZ Biolabs for a free consultation:
Name: Terry
Company: MtoZ Biolabs
Email: marketing@mtoz-biolabs.com
Phone: +1-857-362-9535
Address: 155 Federal Street, Suite 700, Boston, MA 02110, USA
Country: United States
Website: https://www.mtoz-biolabs.com/
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