Publications

This poster demonstrates the utility of the Proteograph™ Product Suite workflow to conduct unbiased, deep, and rapid interrogation of the plasma proteome and to enable large-scale studies to detect novel biological insights. Plasma samples from 100 Alzheimer and 100 healthy matched controls, 1000 injections, and 5,000+ protein groups were analyzed in three weeks using a multi-nanoparticle workflow combined with LC-MS analysis. Classification analysis and pQTL mapping enabled the identification of known and novel plasma biomarkers and showed enrichment for disease-relevant pathways.

This poster demonstrates how the Proteograph™ Product Suite enables deep, unbiased, rapid, and scalable access to the plasma proteome. The study shows the power of the Proteograph in a proof-of-concept proteoform analysis of 80 healthy controls and 61 early-stage non-small-cell lung cancer (NSCLC) samples to infer proteoforms derived from alternative gene splicing or post-translational cleavage. We identified 20 proteoform candidates, including four that showed differential abundance between NSCLC and control samples. This peptide-centric analyses revealed disease-associated proteoforms that were masked with protein-centric analyses.

This poster demonstrates how the Proteograph™ Analysis Suite and Proteogenomics workflow enables user-friendly and reproducible multi-omics analyses of proteomic and genomic data at scale. PAS provides automated data processing and analysis with intuitive, easy-to-interpret visualizations and its Proteogenomics feature integrates genomic variant calls with proteomics data to identify subject-specific variant peptides, offering a comprehensive proteogenomic analysis software suite that facilitates a seamless journey from raw data to biological insight.

This poster demonstrates ultra-high coverage of serum proteins with over 5,000 protein groups identified in a 105-sample cohort and over 3,000 protein groups identified on average per sample. Proteins were quantified at 3-5 fold higher levels compared to depleted and un-depleted serum, with 30% enhanced coverage of low abundant cytokines. This data supports a comprehensive serum proteomics workflow that can be used for patient stratification as well as potential identification of novel biomarkers which are not accessible through other strategies.

This poster describes a multi-omics platform facilitating the evaluation of the global proteome and lipidome in a pancreatic cancer cohort and identified multiple putative biomarker candidates across analyte classes for early disease detection.

This poster demonstractes how comprehensive plasma proteomics profiling of the first all-civilian astronaut crew using the Proteograph Product Suite coupled with LC-MS analysis that offers unique insights to the impact of spaceflight on human health demonstrating even short-term spaceflights can have an impact on human physiology which needs further investigation and monitoring.

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.