Protypia analyzes the protein targets of oncology drugs and the protein pathways and networks in which they function. We use new mass spectrometry technology to quantitatively and precisely measure proteins. Protypia works with pharmaceutical and biotechnology companies from discovery through clinical trials. Our analyses quantify drug targets in preclinical models and human tumor tissue specimens, including formalin-fixed, paraffin-embedded (FFPE) sections and needle biopsies. Our bioinformatics platforms translate our data to practically useful biological interpretation.We partner with client teams to analyze drug targets and identify protein features—proteotypes—that indicate drug susceptibility and system response. We also analyze FFPE tissues from completed clinical trials to retrospectively identify proteotypes associated with trial outcomes, thereby informing the design of future trials. Protypia can collaborate in clinical trial design to reduce the risk of expensive trial failures.
Quantitative analysis of proteins by mass spectrometry provides precision, accuracy and dynamic range unavailable with immunoassay platforms and also enables simultaneous measurement of multiple proteins in a sample. Samples include frozen and FFPE tissues or cells and typically require approximately 100 micrograms of protein (1-2 mg wet weight for fresh./frozen; 1 e6 cells; or 1 cm diameter, 5 micron thickness FFPE section). A principal focus of Protypia is analysis of proteins that control the tumor-immune interface and are immune-oncology (IO) drug targets or critical co-regulators immunotherapeutics. The Protypia platform can simultaneously measure immune checkpoints, co-regulators and immune cell markers, as well as tumor and stromal markers. IO assay menu of over 25 proteins includes PD-L1, PD-L2, LAG3, IDO1, TIM3, VISTA. Incorporation of additional targets upon request. In addition to IO protein panels, multiplexed protein analysis panels focused on other pathways are available.
Quantitative shotgun proteomic analysis provides unbiased survey of protein abundance difference between cell and tissue samples representing distinct phenotypes, disease states, responses to drugs and drug and chemical toxicity. Analysis of 100 micrograms of protein (1 e6 cells; 1-2 mg wet weight frozen tissue; 1-2 FFPE unstained sections of 1cm diameter and 5 micron thickness) typically yields 6,000+ protein identifications. Quantitative estimates of abundance differences of > 2-fold are typically achieved. Shotgun proteomics identifies candidate biomarkers, pathway alterations and changes in gene expression, including unanticipated alterations not manifested at the transcriptome level. Integrative analysis of shotgun proteomics data with genomic, transcriptomic, copy number or other data types enables assessment of multi-level gene regulation.
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