Nanoproteomics

Service Description

BGI has extensive experience in the field of nanoproteomics spanning cellular heterogeneity research across rare cell populations, hard-to-obtain clinical specimens, and pathological tissues.

 

Nanoproteomics

Nanoproteomics refers to quantitative proteomics analysis of small cell populations (typically < 5,000 cells) by the combination of in-situ cleavage and DDA label free technology, and offers possibilities for analysis unavailable with conventional protein extraction and mass spectrometry1.

 

Project Workflow

References

[1] L. Yi, et al., Advances in microscale separations towards nanoproteomics applications, 2017.1523: 40–48.

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Mass Spectrometry Service Specification

Nanoproteomics services are performed using nano-flow liquid chromatography and cutting-edge Orbitrap Fusion Lumos mass spectrometer.

  • Sample Preparation and Services

    Sample Preparation and Services

    • The QC of enzymatic hydrolysis is strictly controlled by LC-MS
    • DDA-Spectral Library generated using HPLC technology and sample fractionation
    • 2h/fraction; 2h for DDA analysis
  • Quality Standard

    Quality Standard

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

    Turn Around Time

    • Typical 5-6 weeks from sample QC acceptance to data report delivery

Sample Requirements

Sample type

Amount

Note*

Library construction
samples-Mammalian cells from similar or adjacent parts

5*10^5

More than 50 μg protein can be extracted

Library construction
samples-Tissue from similar or adjacent parts

10 mg

More than 50 μg protein can be extracted

Nanoscale
samples-Mammalian cells

> 100

Collected cells or tissues (not LCM) with 200 μL low adsorption PCR tube and stored in 2-5 μL PBS solution

Nanoscale
samples-Egg cell or early embryo cell

> 1, and 3-5 is better

Collected cells or tissues (not LCM) with 200 μL low adsorption PCR tube and stored in 2-5 μL PBS solution

Nanoscale
samples-Tissue

1mg

Collected cells or tissues (not LCM) with 200 μL low adsorption PCR tube and stored in 2-5 μL PBS solution

Nanoscale
samples-LCM (Laser capture
microdissection)

Thickness of 10 μm, > 10mm^2

Collected cells or tissues (not LCM) with 200 μL low adsorption PCR tube and stored in 2-5 μL PBS solution

Data Analysis

  • Data analysis and validation performed with Mascot

  • Protein identification and quantification list

  • Cluster analysis of expression patterns across multiple samples

  • Protein GO/COG/KOG/Pathway annotation

  • GO/Pathway enrichment analysis of differential proteins

  • Protein-protein interaction analysis

  • Protein subcellular localization analysis

  • Repeatability analysis

  • Quantitative proteomics and phosphoproteomics correlation analysis

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