Label-free DDA Proteomics

Service Description

Quantitative proteomics refers to the identification and quantification analysis of proteins in two or more samples to obtain the differential expression and function information of relevant proteins. It plays an important research role in the prevention, diagnosis, prognosis and efficacy monitoring of diseases, and can be used to help develop new therapeutic drugs.

Liquid chromatography – tandem mass spectrometry (LC-MS/MS) is currently the best method for unbiased, high-throughput proteomics analysis. In contrast to label-dependent quantitative proteomics such as the iTRAQ method, label-free data-dependent acquisition (DDA) proteomics doesn’t need to use expensive a stable isotope for labeling of proteins. This allows accurate protein quantification of samples without additional error-prone in vitro labelling reactions and enables fast proteome identification and quantification.
In a typical DDA analysis, the mass spectrometer generates a full-scan mass spectra to determine the molecular weights of peptides and then acquires MS/MS spectra on the N most intense peptide ions. Hundreds of MS/MS spectra can be generated in a single run and downstream data analysis tools are applied for peptide identification and quantification. Since the peptides selected for fragmentation are usually the most abundant peaks in the survey scan, it is easy to cause the loss of low abundance peptides.

Label Free DDA Analysis Workflow

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

Research Applications

Disease biomarker research
Drug efficacy evaluation
Special behavior mechanism and food/medicinal value research
Plant growth and development research
Plant disease resistance and insect resistance research
Microbial stress and adversity physiology research

Specifications

  • The QC of enzymatic hydrolysis is strictly controlled by LC-MS
  • 2h for DDA analysis
  • Summary includes all methods and data analysis
  • Reports provided in Excel or PDF format, RAW files available upon request
  • Typical 3-4 weeks from sample QC acceptance to data report delivery

Sample Requirements

Please see the catalogue

Data Analysis

  • 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

Label-free DDA Proteomics

Unique DNBSEQ™ Sequencing Technology

BGI’s Single Cell Sequencing services are typically executed with proprietary DNBSEQ™ sequencing technology platforms, for great sequencing data at some of the lowest costs in the industry. DNBSEQ™ can offer advantages in terms of lower amplification error rates and much lower duplication rates for some sequencing applications. In addition, studies have shown the lower index hopping rate in DNBSEQ™ platforms.