Deep Phosphoproteomics Services

Deep phosphoproteomics is an advanced analytical method based on high-resolution mass spectrometry that systematically and sensitively detects phosphorylation sites in biological samples. As one of the core mechanisms of intracellular signal transduction, protein phosphorylation regulates critical biological processes, including cell proliferation, differentiation, metabolism, and stress responses. However, traditional proteomics approaches fail to capture low-abundance phosphorylation events due to limited coverage. These molecular "switches" are frequently linked to disease mechanisms such as cancer drug resistance, neurodegenerative disorders, and pathogen resistance.

 

Deep phosphoproteomics enables the comprehensive mapping of kinase-substrate regulatory networks, identification of key phosphorylation sites to understand pathway dysregulation, and detailed analysis of dynamic networks. Additionally, it facilitates precise biomarker discovery by identifying phosphorylation features directly associated with clinical phenotypes, such as therapeutic resistance and disease progression. It offers a novel perspective for target discovery, providing data-driven support for kinase inhibitor development and combination therapy strategies.

 

Services at MtoZ Biolabs

At MtoZ Biolabs, we leverage the Orbitrap Astral mass spectrometry platform to deliver cutting-edge Deep Phosphoproteomics Services. Our comprehensive pipeline includes everything from raw data quality control to pathway enrichment and kinase-substrate interaction network visualization, helping researchers decode the‘code’of dynamic modifications and accelerate translational medical research.

 

Analysis Workflow

1. Sample Preparation

• Sample Types: Cells, tissues (frozen/FFPE), biofluids (e.g., plasma, cerebrospinal fluid), or microbial samples.
• Phosphopeptide Enrichment: Optimized protocols to remove high-abundance non-modified peptides, ensuring efficient enrichment of phosphorylation-specific signals.

 

2. Mass Spectrometry Data Acquisition

• Instrumentation: Orbitrap Astral mass spectrometer + ultra-high-performance liquid chromatography (nanoLC).
• Data Acquisition Mode: Data-independent acquisition (DIA) combined with custom isolation window design to maximize ion utilization.

 

3. Data Processing and Deep Analysis

• Database Search: Matching against UniProt/Swiss-Prot and customized PTM databases to ensure precise localization of modification sites.
• Quantitative Analysis: Choice of label-free (DIA) or labeled (TMT/iTRAQ) quantification, adaptable to different experimental designs.
• Functional Annotation: Predicting upstream kinases and generating activity heatmaps, followed by enrichment analysis based on KEGG, Reactome, and Gene Ontology.

 



Figure1. The Workflow of Deep Phosphoproteomics

 

Service Advantages

• High-Sensitivity Detection: Targeting low-abundance phosphorylated peptides, highly efficient enrichment techniques such as metal oxide affinity chromatography (MOAC), immobilized metal affinity chromatography (IMAC), and antibody-based affinity capture are employed in MtoZ Biolabs to enhance the identification of phosphorylated peptides.  
• High-Resolution Mass Spectrometry: Utilizing high-resolution and high-dynamic-range mass spectrometers such as Orbitrap Astral mass spectrometer and Bruker timsTOF Pro, combined with data-dependent acquisition (DDA), data-independent acquisition (DIA), or parallel reaction monitoring (PRM), we enables precise phosphorylation site identification and quantification.
• Flexible Data Delivery: MtoZ Biolabs provides a fully transparent and traceable workflow, from raw spectrum files to customized analytical reports.

 

Applications

1. Cancer Biology and Precision Medicine: Predicting response to targeted therapies and uncover drug resistance mechanisms and Identify phosphorylation-driven immune checkpoint molecules.

2. Neuroscience: Analyzing synaptic plasticity and phosphorylation biomarkers in neurodegenerative diseases.

3. Microbial Drug Resistance Research:Tracking kinase activity changes associated with pathogen antibiotic tolerance.

4. Fundamental Signal Transduction Studies:Constructing kinase-substrate interaction maps and validate novel regulatory nodes.

 

Deliverables

1. Core Data Package

• Raw mass spectrometry files + fully annotated phosphorylation site lists (including site confidence and quantitative values).
• Differential phosphorylation site screening results (volcano plots, heatmaps) and associated kinase activity change reports.

 

2. Analysis Report

• Interactive pathway enrichment maps.
• Kinase regulatory network models and visualization (Cytoscape network diagrams).

 

In an era where dynamic modifications dictate cellular fate, deep phosphoproteomics has become an essential tool for deciphering disease mechanisms and advancing precision therapeutics. MtoZ Biolabs offers internationally leading mass spectrometry platforms, a team with over a decade of kinase research expertise, and a fully integrated bioinformatics pipeline to deliver reliable, high-value Deep Phosphoproteomics Services. Whether you are exploring unknown mechanisms or accelerating drug target validation, we look forward to collaborating with you to unlock the limitless potential of phosphorylation research. Contact the MtoZ Biolabs technical team today to begin your high-dimensional phosphoproteomics journey!