Pro Quantitative Proteomics

With the advancement of protein analysis technology and mass spectrometry performance, DIA quantification methods in proteomics have evolved from the initial DIA to 4D-DIA and then to Astral Zoom DIA. Data analysis has also progressed from initially referencing DDA spectral libraries to database-independent retrieval and then to combining machine learning to assist in the analysis of raw DIA mass spectrometry spectra. This has enabled DIA quantification to combine the advantages of high throughput, high depth, and high accuracy, making it the mainstream analytical technique in proteomics analysis. Its application range covers routine samples, clinical samples, trace samples, and single-cell samples.

DDA & DIA

The DDA method randomly selects and prefers peptides with high signal intensity for fragmentation and data acquisition, making the identification and quantification of low-abundance peptides a significant challenge. The DIA method divides all peptides into several windows based on molecular weight, without distinguishing peptides within each window by abundance. All peptides within a window are fragmented and data acquired together, ensuring comprehensive and consistent mass spectrometry data collection for all peptides.

Schematic diagrams of DDA and DIA methods. All mass spectra acquired by DDA originate from high-abundance single peptides, while DIA acquires mixed peptide spectra containing low-abundance peptides

Pro-DIA（4D）

Pro-DIA (4D) is a DIA technology based on the timsTOF HT ion mobility platform. It adds a fourth dimension—ion mobility—to traditional DIA. Ion mobility primarily separates ions based on their shape and cross-section, enabling the differentiation of peptides with very small m/z differences, thus allowing the identification and recognition of low-abundance protein signals. Combining PASEF (Parallel Accumulation Serial Fragmentation) and TIMS (Ion Mobility Spectroscopy), Pro-DIA allows for repeated measurement of the collision cross-section (CCS) of all detected ions, enabling faster and more sensitive qualitative and quantitative proteomics analysis. Compared to traditional methods, it comprehensively improves protein identification coverage, reproducibility, and quantitative accuracy.

4D-DIA Analysis Flowchart

Plus-DIA（Zoom）

Astral Zoom, an upgraded version of Astral, achieves a perfect balance of high throughput, deep coverage, high sensitivity, and high reliability in quantification. The Plus-DIA quantitative omics platform enables deeper identification with fewer samples, supporting more comprehensive protein sequence coverage and pathway annotation, thereby revealing more biological information.

Compared to the Astral mass spectrometer, the Astral Zoom mass spectrometer offers greater depth of coverage for proteins and peptides.

(Data source: Official website)