Differences and Characteristics of Targeted Proteomics and Discovery Proteomics
Proteomics research strategies can be divided into discovery proteomics and targeted proteomics. Discovery proteomics focuses more on protein screening and dynamics, while targeted proteomics is more focused on detecting target proteins/peptides for absolute quantification.
Targeted proteomics analysis strategies
SRM/MRMTwo-stage ion selection eliminates most interfering ions. Chemical interferences in mass spectrometry are reduced, significantly improving the signal-to-noise ratio of the target detector, thereby achieving high detection sensitivity.
PRMIt can simultaneously quantify 50 proteins within an hour without using antibodies. Comprehensive scanning of product ions can be easily accomplished without selecting ion pairs and optimizing fragmentation energy. PRM can detect all target ions from the transition of target ion fragment detection, reducing workload and achieving higher resolution.
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MRM/PRM quantitative proteomics
Applications of targeted proteomics
1. Targeted proteomics is used for in-depth analysis and quantitative measurement of selected proteins in biological samples.
2. Used as an auxiliary tool in the ligand binding assay (LBA) field of monoclonal antibody (mAb) dosage pharmacokinetics (PK).
3. Systems biology and clinical proteomics research.
4. Predict transporter-mediated drug clearance and facilitate new drug development.
Discovery proteomics analysis strategies
SWATH-DIA is suitable for high-throughput large-scale protein quantitative analysis. The peak information of MS1 precursor ions and MS2 fragment ions is very complete, requiring retrospective analysis. It can be easily operated without grouping. The number of quantified peptides in SWATH-DIA has greatly increased, which increases the number of quantifiable proteins and the sequence coverage of detected proteins.
In MSX-DIA, the mass range is divided into narrower precursor isolation windows, each typically about 4 m/z wide, allowing collection of all ion and fragment spectra without losing any information. The data is easier to track, and even if certain proteins or compounds cannot be found at the current level, they can be traced back later.
The purpose of discovery proteomics is to gather information about all proteins and protein structures in biological samples. Utilizing the information obtained from the samples, discovery proteomics can identify thousands of proteins and protein structures in a single experiment.
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Applications of discovery proteomics
1. Host cell protein analysis;
2. Chemical modification analysis;
3. Biomarker discovery;
4. Drug target discovery.
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