Deep-Dive DIA Phosphoproteomics

Protein phosphorylation serves as a critical regulatory mechanism in cellular life activities, precisely modulating protein function through reversible chemical modifications. This process acts as a central hub in cellular signaling networks, directly influencing gene expression regulation, metabolic pathway activity, and cellular responses to external stimuli. Continuous innovations in modern mass spectrometry technology have propelled phosphoproteomics research into a new developmental phase. Advanced methods based on Data-Independent Acquisition (DIA) strategies, combined with efficient phosphopeptide enrichment techniques, have significantly improved the coverage breadth and data reproducibility of phosphorylation site identification. The new generation of phosphoproteomics platforms enables systematic, high-throughput site resolution in complex biological samples, providing powerful technical support for in-depth exploration of dynamic cellular regulatory networks.

Figure 1. Model architecture and performance of DeepPhospho. (Source: Lou R, et al. 2021)

Deep-Dive DIA Phosphoproteomics integrates ion mobility separation technology with high-precision mass spectrometry platforms, effectively distinguishing structurally similar modified peptides through multi-dimensional separation strategies. While significantly enhancing identification sensitivity, it establishes a solid foundation for accurate quantitative analysis. This technology is particularly suitable for limited precious samples and dynamic process monitoring research needs, providing unprecedented molecular insights for life science research.

Service Offerings

Creative Diagnostics provides comprehensive Deep-Dive DIA Phosphoproteomics analysis services, covering systematic identification of phosphorylated proteins and their corresponding sites in samples. Utilizing label-free quantification technology based on ion mobility separation, we enable precise differential analysis of phosphorylation levels across different samples, ensuring data reliability and accuracy. Additionally, we offer end-to-end solutions tailored to specific client needs—from basic identification to in-depth bioinformatics analysis—including specialized technical services such as precise identification of phosphorylation modification sites, accurate quantification of modification levels, and kinase-substrate network regulation analysis.

Service Advantages

• Excellent Detection Sensitivity and Coverage Depth: Based on ion mobility separation technology combined with efficient enrichment strategies, enabling deep detection of low-abundance phosphorylated proteins
• High-Quality Data Output: Leveraging high-resolution mass spectrometry platforms to ensure accurate identification results and reliable quantitative data
• Extensive Project Experience: Years of proteomics service experience providing professional guidance from experimental design to result interpretation
• Standardized Operational Procedures: Established comprehensive quality control systems ensuring experimental process reproducibility and data comparability
• One-Stop Solution: Providing end-to-end services from sample preparation to bioinformatics analysis, saving client time and resources

Service Workflow

Considerations

Sample Requirements

• Animal Tissues: Recommended amount ≥50mg
• Cell Samples: ≥1×10⁷ cells
• Plant Samples:
  • Model plants: Arabidopsis, rice, tobacco, etc.
  • Crops: Soybean, corn, quinoa, cotton, etc.
  • Fruits and vegetables: Tomato, citrus, etc.
  • Medicinal plants: Salvia miltiorrhiza, alfalfa, etc. (fresh tissues)
  • Minimum leaf tissue: 100 mg

Final Deliverables

Clients will receive the following analysis results:

• Complete Experimental Report: Including detailed experimental procedures and proteomics identification/quantification results
• Standard Bioinformatics Analysis:
  • Modified protein and modification site identification results
  • Identification feature distributions: peptide length, protein coverage, unique peptide distributions
  • Modification site motif prediction
  • Protein GO functional classification and Pathway annotation
• Advanced Bioinformatics Analysis:
  • Protein-protein interaction network analysis
  • Protein domain prediction
  • Protein subcellular localization prediction

Through our professional Deep-Dive DIA Phosphoproteomics service, you will obtain comprehensive and precise phosphorylation regulatory network information, providing reliable data support and innovative research directions for your scientific investigations. Our expert team offers comprehensive technical support from experimental design to result interpretation, ensuring the smooth progress of your research projects.