Publications

This poster demonstrates how the Proteograph Product Suite and Zeno SWATH DIA acquisition workflow that facilitates identification and quantification of thousands of proteins from human plasma without compromising throughput or reproducibility, creating a unique opportunity to detect robust protein biomarkers that translate into viable clinical tests for complex diseases.

This poster demonstrates that DIA-NN, combined with the cloud-based large group run, more sensitively identifies protein groups across the cohort, which has resulted in the identification of ~4000 protein groups across a 141 NSCLC study with a microflow SWATH method and enhanced classification performance and stability with VAE, Random Forest, and SVM to AUC-ROC 0.95 compared to previous studies, leading to better biomarker discovery and disease characterization using deep and unbiased plasma proteomics analysis at scale.

This poster demonstrates the application of the Proteograph™ Product Suite to study differentially expressed post-translational cleaved proteoforms using a modified COPF and Wilcoxon’s rank test in a NSCLC biomarker study. This study highlights the fact that differential expression are sometimes found at the peptide level and not at the protein level due to the presence of protein variants in population-scale studies.

This poster demonstrates the Proteograph™ Product Suite enables rapid, automated, and reproducible sample preparation for deep plasma proteomics analysis in large cohort plasma proteomics studies.

This poster demonstrates the Proteograph™ Product Suite provides a deep and untargeted proteomics workflow for conditioned media with less sample volume required, enabling rapid and automated sample preparation for large-scale conditioned media proteomics analysis and enhanced proteome depth across different protein functionality.

This poster presents the Proteograph™ Analysis Suite (PAS), a cloud-based intuitive, scalable, data informatics solution that enables a seamless journey from raw LC-MS data to biological insight and supports automated data upload, data processing, integrated database search engines (both DIA and DDA LC-MS data), and visualization tools.

This poster demonstrates a next-generation platform capable of analyzing large cohort proteomics studies in hours, supporting fleets of LC-MS instruments by integrating legacy scoring algorithms with distributed processing infrastructure. These spark-accelerated workflows are supporting thousands of group run analyses, enabling analysis of hundreds of terabytes of LC-MS data generated in large cohort group runs.

This poster demonstrates batch effects can contribute to a large amount of the noise in large-scale proteomics datasets compared to biological variations, but deep learning approaches have the ability to integrate diverse proteomics datasets, and the extension of DANN can harmonize data across technical factors while maintaining the fidelity of the biological signal in the data.

This poster demonstrates the Proteograph™ Product Suite facilitates access to lower abundant proteins in the plasma proteome compared to neat plasma digestion, for high-throughput unbiased plasma proetomics analysis.

This poster demonstrates the Proteograph™ Product Suite provides a significant increase in the peptide group and protein group counts versus neat plasma, using a robust high throughput 33min microflow DIA method.