Targeted Proteomics Analysis

Targeted Proteomics Analysis

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CD Genomics is a global bioinformatic analysis service provider. We provide customers with targeted proteomics bioinformatic analysis services, helping researchers quantify different proteins in samples quickly and accurately. Once we receive your data, we will be start the data analysis and provide you the most easy-to-interpret analysis result report.

Introduction of Targeted Proteomics Analysis

Targeted proteomics quantitative technology can make up for the lack of quantitative sensitivity and randomness of non-targeted quantitative omics, and has the advantages of high throughput, high accuracy, and repeatability. Targeted proteomics quantitative technology mainly includes PRM and MRM/SMR.

Targeted proteomics quantitative technology can be used for signal transduction pathway detection, tumor marker research and post-translational modification research. It is another fast and efficient protein targeted quantitative technology besides antibody-based protein quantitative technology. With the deepening of proteomics research, differential proteomics has become more popular. The use of bioinformatic methods to quantify and analyze data of targeted proteomics will help to discover potential disease markers and accelerate the pace of clinical application of proteomics.

Schematic diagram of targeted proteomics technology - CD Genomics.Fig 1. Schematic diagram of targeted proteomics technology.

  • Data analysis
  • PRM
  • MRM

What we can do

CD Genomics provides quantitative analysis of proteomics data generated by different target protein quantitative technologies (including PRM and MRM). In addition, we will also provide joint analysis between proteomics and other omics. Other than general data analysis, we can also provide customized data analysis and chart production services and provide one-stop solutions for your research.

Application Field

Verification of the results of non-targeted proteomics such as iTRAQ and Label-free.

Absolute quantitative research on multiple proteins or peptides simultaneously.

Qualitative and quantitative research on protein post-translational modification.

Absolute quantitative study of biological targets.

Advantages of Targeted Proteomics

Targeted proteomics does not rely on antibodies. Quantitative analysis can be directly performed on the target protein or peptide.

High specificity: targeted detection of target protein or peptide.

High accuracy and sensitivity.

High throughput: detecting multiple proteins simultaneously.

Wide application range and good repeatability.

The cycle is clear, the risk is controllable, and the experimental results can be predicted.

CD Genomics Data Analysis Pipeline

CD Genomics quasi-targeted metabolomics data analysispipeline - CD Genomics.

Bioinformatics Analysis Content

The targeted proteomics data analysis service provided by CD Genomics has strict data quality control and standardized analysis procedures, and the analysis results can be repeated. In addition, customized charts can be directly used for article publication.

Standard information analysis Spectrum analysis,
Protein data quality evaluation
PCA analysis of multi-component samples
Protein function annotation, including GO function annotation, KEGG function annotation and COG function annotation
Statistical analysis of differentially expressed proteins
Cluster analysis of differentially expressed proteins, including hierarchical clustering and K-means clustering
Protein interaction network analysis based on STRING database
Customized information analysis Multi-omics joint analysis
Other customized information analysis

For targeted proteomics data analysis,the content of customized information analysis services can be negotiated and determined based on the needs of customers. If you have any questions, please click online inquiry.

CD Genomics provides general analysis and customized analysis of targeted proteomics data for different types of targeted proteomics data. In addition to quantitative analysis of PRM and MRM targeted protein data, other targeted protein data such as SWATH/DIA data can also be performed. We will provide you with satisfactory data analysis services. If you are interested in our services, please feel free to get in touch for more detailed information.

Introduction of PRM

PRM (Parallel Reaction Monitoring) technology is a targeted verification proteomics technology based on mass spectrometry. Through selective detection of specific peptides or target peptides, targeted relative or absolute quantification of target proteins or modified peptides can be achieved . Its advantage lies in overcoming the difficulty of antibody preparation and the difficulty of buying antibodies, and it perfectly replaces antibody-based Western blot, ELISA and other technologies. PRM can be used for the verification of wide-screen data, such as genome, transcriptome, quantitative proteome, target protein or peptide obtained by modifying the proteome, to achieve relative or absolute quantitative analysis of protein or peptide.

Workflow for highly multiplexed, RT scheduled sPRM assay development.Fig 1.Workflow for highly multiplexed, RT scheduled sPRM assay development. (Birgit S, et al.2015)

Technical Principle

PRM technology is based on a high-resolution, high-precision mass spectrometer (such as Q-Exactive HF-X). First, it uses the selective detection capability of a quadrupole mass analyzer to selectively detect the precursor ion information of the target peptide. Then it fragments in the HCD collision cell, and finally enters the high-resolution, high-quality precision Orbitrap analyzer to detect all fragments in the selected precursor ion window. In this way, the target protein or peptide in the complex sample can be accurately analyzed.


  1. Birgit S, et al. Multiplexed, scheduled, high-resolution parallel reaction monitoring on a full scan QqTOF Instrument with Integrated data-dependent and targeted mass spectrometric workflows[J]. Analytical chemistry, 2015, 87( 20):10222.

Introduction of MRM

Multiple reaction monitoring technology. Multiple reaction monitoring (MRM) technology was also called selective reaction monitoring (SRM) in the early days. This technology is essentially a scanning mode of mass spectrometry. Based on the specific parent ion and product ion pairs of the target protein, signals that conform to the target ion rules are selected to remove signal interference that does not conform to the rules. Finally, a high-sensitivity, high-accuracy and specific targeted protein quantitative analysis is performed.

Advantages of MRM

High sensitivity. After two-stage mass spectrometry, the ions that are consistent with the target ion are selected to eliminate interfering ions, which greatly improves the signal-to-noise ratio and improves the accuracy of detecting target ions.

With high throughput, more than 200 proteins can be identified at one time.

Absolute quantitative analysis can be performed without relying on antibodies.

Identify low-abundance proteins with high precision, with a quantitative range spanning 4 orders of magnitude.

Technical Principle

MRM mass spectrometry analysis mainly includes three stages.

1. First-level mass spectrometry scans to screen out parent ions with the same specificity as the target molecule;

2. Collision to fragment precursor ions and remove interfering ions;

3. Collect only the mass spectrum signal from the selected specific ion.

* For Research Use Only. Not for use in diagnostic procedures.
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