PTM Proteomics

Description
Specification
Resources

Service Description

We have developed innovative solutions for optimizing the processes of PTM identification of purified protein, modified protein profiling, and protein PTM quantification in complex biological matrices and other complex mixtures.

PTM Proteomics

Post-translational modification (PTM) of proteins refers to the chemical changes proteins may undergo after translation. Common PTMs include Phosphorylation, Glycosylation, Acetylation and Ubiquitination. As a result, identifying and understanding PTMs is key for the study of cell biology and the treatment and prevention of disease.

BGI Genomics has extensive experience in the field of PTM Proteomics1,2 and has developed reliable workflows using market leading technologies and an advanced bioinformatics infrastructure.

Project Workflow

Phosphorylation:


Acetylation/Ubiquitylation:

  • Protein extraction
  • Protein digestion
  • Modified peptides enrichment
  • HPLC fractionation
  • LC-MS/MS (DDA)
  • Data analysis

Glycosylaion:

Quantification of N-glycosylated peptides
  • Protein extraction
  • Protein digestion
  • Modified peptides enrichment
  • Remove glycan chains
  • LC-MS/MS(DDA)
  • Data analysis
Quantification of N-intact glycopeptides
  • Protein extraction
  • Protein digestion
  • Isobaric labeling and enrichment
  • HPLC fractionation
  • LC-MS/MS
  • Analysis by StrucGP

References

[1] Zhang, Y., et al., Evidence for Differential Glycosylation of Trophoblast Cell Types. Mol Cell Proteomics, 2016 Jun;15(6):1857-66. doi: 10.1074/mcp.M115.055798.

[2] Hao P L, et al., Correction of Errors in Tandem Mass Spectrum Extraction Enhances Phosphopeptide Identification. J. Proteome Res., 2013, 12, 12, 5548–5557. doi: 10.1021/pr4004486.


Mass Spectrometry Service Specification

PTM Proteomics services are performed using nano-flow liquid chromatography and cutting-edge mass spectrometer (Q Exactive HF/HF-X and Orbitrap Fusion Lumos).

  • Sample Preparation and Services

    • Digestion performed using sequencing-grade trypsin
    • Off-line sample fractionation using HPLC technology
    • Each fraction analyzed using nano-flow LC-MS/MS
    • TiO₂/ZrO₂ enrichment for phosphoproteomics; CST antibody enrichment for acetylated/ ubiquitylated proteins; MAX column enrichment for glycosylated proteins

  • Quality Standard

    • Summary includes all methods and data analysis
    • Reports provided in Excel or PDF format, RAW files available upon request

  • Turn Around Time

    • Phosphorylation Turn Around Time from sample QC acceptance to data report delivery 3-5 weeks
    • Glycosylation Turn Around Time from sample QC acceptance to data report delivery 4-5 weeks
    • Acetylation/Ubiquitylation Turn Around Time from sample QC acceptance to data report delivery 3-5 weeks

Sample Requirements

Data Analysis

DATA ANALYSIS

    • Data analysis and validation performed with Mascot

    • Protein PTM identification

    • Protein PTM quantification

    • Modified protein function annotation

    • Differential modified protein function enrichment

    • Kinase prediction analysis

    • Motif distribution of PTM sites

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