Quantitative Analysis of Low-Abundance Proteins Using DIA-PRM

In modern biological research, the quantitative analysis of low-abundance proteins has always been a challenge. These proteins are usually present at extremely low concentrations in biological systems, but they play crucial roles in various physiological processes, disease progression, and drug responses. As a result, accurately and efficiently quantifying these low-abundance proteins has become a hot and challenging topic in proteomics research. To address this challenge, researchers have introduced various techniques, among which the combination of Data-Independent Acquisition (DIA) and Parallel Reaction Monitoring (PRM) has emerged as a powerful tool for quantifying low-abundance proteins.

 

Data-Independent Acquisition (DIA) is an emerging mass spectrometry acquisition mode that differs from traditional Data-Dependent Acquisition (DDA) by fragmenting and detecting all peptides simultaneously. In DIA mode, the mass spectrometer scans predefined windows, and all peptides within each window are fragmented simultaneously to generate MS/MS spectra. This acquisition mode significantly increases data throughput and coverage. The advantage of DIA lies in its ability to capture all possible peptide information, thereby improving the detection sensitivity for low-abundance proteins.

 

Parallel Reaction Monitoring (PRM) is a targeted mass spectrometry-based quantitative method. PRM operates similarly to traditional Selected Reaction Monitoring (SRM), but the key difference is that PRM performs parallel detection of all fragment ions of the target ion using a high-resolution, high-accuracy mass spectrometer. This feature allows PRM to achieve higher specificity and accuracy, especially when quantifying low-abundance proteins in complex samples, as PRM can significantly reduce noise interference and improve quantification precision.

 

Advantages of Combining DIA and PRM

In proteomics, the combination of DIA and PRM offers a powerful approach for the quantitative analysis of low-abundance proteins. First, the comprehensive peptide information acquired by DIA can be used for subsequent targeted quantification by PRM. This means that through the initial screening with DIA, we can identify low-abundance proteins of interest and then use PRM for precise quantification. The DIA-PRM approach not only addresses the specificity issues that may arise in DIA quantification but also retains the high precision of PRM in detecting low-abundance proteins.

 

Another important advantage of combining DIA and PRM is its ability to significantly enhance the sensitivity and coverage of quantification. DIA can identify and detect more proteins, while PRM’s high-resolution mass spectrometry ensures accurate quantification of low-abundance proteins. This combination is particularly suitable for the analysis of complex biological samples, such as plasma and tissue homogenates, effectively overcoming interference from complex matrices.

 

Application Examples of DIA-PRM in Quantifying Low-Abundance Proteins

The DIA-PRM combination has been widely applied in the quantitative analysis of low-abundance proteins. For example, in cancer research, DIA-PRM has been used to quantify cancer biomarkers in the blood. These biomarkers often exist at extremely low concentrations in plasma, and by combining DIA and PRM, researchers can simultaneously perform high-throughput biomarker screening and high-precision quantification, providing a valuable tool for early cancer diagnosis.

 

Additionally, the DIA-PRM technique has been used to study biomarkers in neurodegenerative diseases. In diseases like Alzheimer’s, certain low-abundance proteins associated with pathology may change in the early stages. Through DIA-PRM technology, researchers can accurately capture these changes from complex biological matrices, aiding in early disease diagnosis and treatment monitoring.

 

The DIA-PRM combination offers a powerful solution for the quantitative analysis of low-abundance proteins. It combines the high throughput and coverage of DIA with the high specificity and accuracy of PRM, effectively addressing the challenges of quantifying low-abundance proteins in complex biological samples. In the future, as technology continues to advance, the application prospects of DIA-PRM in biomedical research will become even broader.