label-free dia quantitation


service description

bgi genomics participates in quantitative performance assessment as well as standardization and harmonization of multi-national dia proteomics analysis supporting precision medicine studies. we have developed innovative solutions for optimizing the process of accurately quantifying proteins in complex biological matrices and other complex mixtures.

label-free dia quantitative proteomics

data-independent acquisition (dia) is a label-free quantitative technique which provides highly consistent quantitation and broad proteome coverage¹. we create a customized spectral library with your specific sample and then analyze individual samples using nano-flow lc-ms/ms with dia scanning and quantitation². label-free dia quantitative proteomics service is ideal for long-term projects or projects with large sample sets which require accurate and reproducible quantitation.

project workflow

  • sample preparation
  • hplc fractionation
  • lc-ms/ms dda analysis
  • dda library generation and updates
  • lc-ms/ms dia analysis
  • quantitation and bioinformatics


[1]. wong, j. w. h., & cagney, g. (2009). an overview of label-free quantitation methods in proteomics by mass spectrometry. proteome bioinformatics, 273–283.doi:10.1007/978-1-60761-444-9_18. [2]. searle bc, pino lk, egertson jd, ting ys, lawrence rt, maclean bx, villén j, maccoss mj. chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. nat commun. 2018 dec 3;9(1):5128. doi: 10.1038/s41467-018-07454-w.

mass spectrometry service specification

  • sample preparation and services

    • the qc analysis of enzymatic hydrolysis is strictly controlled by lc-ms
    • dda-spectral library generated using hplc technology and sample fractionation
    • 2h/fraction for non blood; and 2h/fraction for non-human blood; 1h/fraction for human blood
  • quality standard

    • summary includes all methods and data analysis
    • reports provided in excel or pdf format, raw files available upon request
  • turn around time

    • typical 4-5 weeks from sample qc acceptance to data report delivery

sample requirements

we accept protein samples in a variety of formats. for attaining maximum proteome coverage we recommend utilizing our sample fractionation services, performed using our off-line uhplc-uv platform.
sample typeamount and concentrationminimum sample volume
protein sample in liquid solutionrecommended 400 µg with fractionation: 2 µg/µl200 µl
protein sample in liquid solutionminimum required 100 µg with fractionation: 1 µg/µl100 µl

data analysis

advanced bioinformatics
  • data analysis and validation performed with mascot
  • protein identification and quantification list
  • differential proteins data statistics and volcano plot
  • principal component analysis (pca) and cluster analysis
  • protein go/cog/kog/pathway annotation
  • go/cog/kog enrichment analysis of differential proteins
  • protein-protein interaction analysis
  • protein subcellular localization analysis
  • time series analysis
  • repeatability analysis
  • quantitative proteomics and phosphoproteomics correlation analysis