Sonata Biosciences Inc — Department of Health and Human Services SBIR Phase I: 400

Description

Abstract Bottom up proteomics is a technique where proteins from a sampleincluding complex human fluidsand tissue and cell samplesare digested enzymatically into its constituent peptides before analytical characterization is performed using liquid chromatography tandem mass spectrometryFrom these peptide fragmentsthe protein mixture contained in the original sample are reassembledidentifiedand quantifiedif desiredIt is the predominant method used for protein analysisand it is used broadly to uncover genetic expression of proteins and their variants in a system of interestincluding differential expression to determine for the presence of disease and for the efficacy of disease treatmentThere are many steps between the initial protein isolation and injection onto the liquid chromatograph for mass spectrometry analysisThe goalof courseis that the final assembled proteins reflect accurately the proteins contained in the original sampleThe weakest step appears to be the final purificationwhich uses a reverse phase adsorbentRecoveries here for a reference sample are only aboutand this is reflected in the sequence coverage of the reassembled proteinsHere we propose an alternative based on an unconventional electrophoresis methodIt offers a much more complete peptide recovery that has the potential to substantially eliminate peptide biasThe new method offers a means to concentrate by at leastfold while removing impurities such as saltsdenaturants such as ureareducing agents such as dithithreitoland most surfactantsIf successfulthis peptide recovery method should enable more complete and useful protein characterization of a sample of interest Narrative Bottom up proteomics is an analytical technique that is the cornerstone of proteomics researchProteins and their variants have implications for disease discovery and monitoring its progressionfor disease diagnosisand for the efficacy of companion diagnosticsIt relies on many intermediate steps between sample procurement from whatever source to convert it to a form suitable for characterization by liquid chromatography electrospray tandem mass spectrometryWe have identified the weakest link in those stepsthe final peptide purification and isolationand propose to develop a powerful alternative method to recover a sample that will reflect more accurately the proteinsprotein fragments and variants the initial sample containsWe believe that it will have a profound effect on determining disease and its progression by providing protein data that is of much higher quality and without the bias that often is present using existing methodsThisin turnwill enable improved fundamental disease understandingand facilitate improved disease diagnostics and development of therapeutics against those diseases