Digital Proteomics was launched in 2009 with an audacious business start-up strategy: Develop unique computational tools in a burgeoning life science field that has an abundant need for data analyses which no one has yet provided.
The company was founded by three UC San Diego computer scientists who are leaders of the campus’s NIH Center for Computational Mass Spectrometry: Pavel Pevzner, Ph.D., Vineet Bafna, Ph.D., and Nuno Bandeira, Ph.D. Bafna also directs the UCSD Bioinformatics and Systems Biology Ph.D. Program. One of his Ph.D. students, Natalie Castellana, was in the early stages of her doctoral studies when she and Bafna began collaborating in the relatively new field of mass spectrometry-based proteomics, which is the study of the entire set of natural proteins.
With funding from an Integrative Graduate Education and Research Training (IGERT) grant from the National Science Foundation, Castellana focused her proteomics research on new applications of peptide mass spectrometry. “Proteomics is one of the fastest classes of pharmaceuticals entering the market,” she said. “But we don’t yet have the same computational tools for analyzing proteins as we have for analyzing the genome.
“People see genomics as the next step in personalized medicine,” she added. “But the genome is a static picture of what is happening in your body; it always stays the same. Proteins change dramatically based on what is happening in your environment or what you are eating. Analyzing your proteins gives you a personalized view of what’s going on inside your body.”
One of Digital Proteomics’ breakthrough ideas has been its patented Spectral Network approach that analyzes molecules by organizing them into network structures that will reveal similar spectra. It can be used to organize complex samples of a wide range of molecules including peptides and metabolites
“With this approach, instead of looking at one spectrum at a time, you look for correlations between spectra, and you analyze them in concert to find spectra of molecules that are related,” said Castellana, who formally joined Digital Proteomics after she earned her Ph.D. in 2012. “This way, we can analyze and figure out much more about the molecules than we could previously discover, and we avoid doing work that we already have done.”
Early findings by the Digital Proteomics team triggered immediate interest. Their paper on re-annotating the corn genome using mass spectrometry in the journal Molecular and Cellular Proteomics was hailed as the “bioinformatics paper of 2013″ by the blog News in Proteomics Research, which urged readers, “If you are working with an organism that is not fully sequenced, or you want to but the lack of sequencing is stopping you, definitely check out this paper.”
Said Castellana, “After we had a couple of collaborations, as soon as the papers were published, people came out of the woodwork wanting to work with us.”
Today, Castellana is Chief Technology Officer at Digital Proteomics, and the company is financing its growth through sales to and co-developments with biotech firms. “To give one example, we’ve worked closely with Genentech to develop our antibody sequencing tool, Valens,” she said.
“Our goal is to generate more refined products that serve specific needs of pharmaceutical companies,” she continued. “For almost all the tools we make, we don’t have any real competitor, and this sets us apart. With these tools, proteomics will become the star of drug discovery that everyone knows it can be.”
Natalie Castellana, Ph.D
Department of Computer Science and Engineering
Chief Technical Officer of Digital Proteomics