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Innovative "Wide Window Acquisition" Boosts Proteome Coverage by Nearly 40%

MicrOmics Technologies, a pioneer in the field of proteomics, is elated to share groundbreaking results from Kelly's group's recent study titled "Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics". The publication underscores the immense potential and success of the novel wide window acquisition (WWA) technique in boosting proteome coverage.

Key Highlights from the Study:

  • Efficient Sample Preparation: By synergizing efficient sample preparation with ultra-low-flow liquid chromatography, the team was able to achieve significant advancements in single-cell proteomics.

  • Introduction of WWA: The newly introduced WWA approach deploys large isolation windows, ensuring intentional co-isolation and co-fragmentation of neighboring precursors with the chosen precursor. This novel method marks a significant leap in proteome analysis.

  • Impressive Proteome Coverage: With WWA, the number of MS2-identified proteins saw a surge of approximately 40% in comparison to the conventional data-dependent acquisition. Remarkably, using a 40-minute LC gradient at roughly 15 nL/min, the team identified an average of 3,524 proteins per single-cell-sized protein digest aliquot. Even when the gradient was reduced to 20 minutes, proteome coverage only witnessed a slight 10% dip.

  • Comparative Analysis of HeLa Cells: Utilizing this advanced platform, the research team delved deep into the proteome of single HeLa cells with an essential autophagy gene, atg9a, knocked out. They compared the findings with the isogenic WT parental line. The outcomes showcased almost identical proteome coverage with a striking observation of 268 proteins being significantly upregulated or downregulated. Notably, upregulated proteins were predominantly linked to innate immunity, vesicle trafficking, and protein degradation.

This trailblazing research by Dr. Kelly's group paves the way for deeper insights into single-cell proteomics, propelling the field forward and opening new avenues for comprehensive proteome analysis.

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