Lukas Reiter (Biognosys)
Label-free data independent acquisition (DIA) has enabled deep querying of the proteome and become the method of choice for large-scale proteome profiling. From the very beginning, Spectronaut has been at the forefront of the development of DIA data analysis and visualization. In its 10th year anniversary, Spectronaut is the most widely cited software tool for DIA data analysis.
Here, we provide an overview of the latest improvements available with Spectronaut 15, and also an outlook of where we see Spectronaut and the field progressing. By making use of the latest developments in MS instruments and new technologies like deep learning, we see an exciting roadmap ahead for both DIA and Spectronaut.
We hope to excite you with the promise of an even deeper and more quantitative measurement of the proteome in biologically relevant workflows in the future.
Brett S. Phinney (UC Davis, Genome Center – Proteomics Core Facility)
Academic core facilities have several unique challenges. Foremost is how to maximize biologically meaningful data for a wide variety of collaborating biologists while minimizing cost and turnaround time. Although these challenges are not necessarily unique to core facilities, often core facilities deal with a wide variety of organisms and questions that that need to be answered quickly. Here I will present several recent projects from a wide range of collaborators and how we used DIA and Spectronaut to streamline and acquire data as efficiently as we currently can. Several features, in particular, will be explored such as generating and using DIA and DDA libraries across multiple projects, maximizing data for fast LC runs for large numbers of samples, and using Spectronaut’s post-analysis visuals for diagnosing potential problems with your datasets.
Short-Bio Lukas Reiter (Biognosys)
Lukas graduated from ETH Zurich in molecular biology. For his PhD, he joined the groups of geneticist Michael Hengartner and proteomics pioneer Ruedi Aebersold and received his degree in 2009 from the University of Zurich. After that Lukas joined Biognosys in 2010 as one if its first employees. As CTO, he oversees research as well as product and workflow development at Biognosys. Lukas is fascinated by proteomics technology and the idea of making it available to everybody who needs to know about proteins.
Short-Bio Brett S. Phinney
Brett Phinney received his Ph D. from the University of Texas at Austin where he used mass spectrometry to study the protein conformation of the viral spike protein complexes of a virus similar to SARS-CoV-2 way back in the mass spectrometry dark ages circa 2000. After receiving his Ph D. he did a Postdoc with noted mass spectrometrist Jack Watson at Michigan State University. From there he became the assistant director of the newly formed Michigan Proteome Consortium and became the director of the new Michigan State proteomics core facility. In 2005 Brett accepted the position of the Director of the new UC Davis Genome Center Proteomics Core facility where he designed and established the new core on campus and has been there ever since. Brett has also taught proteomics at a number of institutions including Michigan State University, and Cold Spring Harbor, and UC Davis, where he teaches an intense summer short course every summer.
The UC Davis Genome Center Proteomics Core, has a staff of four dedicated scientists. The Proteomics Core provides state-of-the-art LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics, and Post Translational Modification analysis for clients on and off-campus. We provide services at a reasonable rate (we try and breakeven) and a reasonable turnaround time
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