Lukas Reiter (Biognosys)
With Spectronaut 18 we solve most of the pain points of modern mass spectrometry-based projects. With studies growing, software tools that support the increasing need for computational power are essential. Spectronaut 18 is cloud-ready and comes with long-awaited Linux support to solve hardware scalability bottlenecks. But that’s not the only improvement we’ve made. With all the unexplained features coming from the mass spectrometers, we won’t stop until we extract the last bits of valuable information from our LC-MS runs. With Spectronaut 18, we made good progress in that direction, and we achieved significant increases in the number of identification as well as quantification quality. Finally, we’ve further improved and added new features to the user interface of Spectronaut.
Greg Potts (AbbVie)
Drug discovery relies on robust chemical biology workflows to quantify drug-target engagement, identify potential off-targets, and characterize therapeutic mechanism-of-action. While these workflows have typically utilized chemical labeling approaches, recent advances in MS instrumentation and software have fueled transition to DIA MS and produced a consequent increase in proteome study sizes due to higher throughput data acquisition. One increasingly crucial aspect of lab productivity relies on computational bandwidth to analyze DIA data that is being generated at an expanding rate. Here we present our benchmarking of Biognosys Spectronaut 18 software utilizing Amazon Web Services (AWS) with Windows and Linux formats. We find that Spectronaut data search times are reduced when using AWS instances tailored with sufficient RAM and multicore processing, particularly for large proteome datasets. We will also highlight recent work using our DIA platform for Activity Based Protein Profiling (ABPP) of covalent fragments to ligand reactive cysteines within the proteome.
Short Bio Lukas Reiter:
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 of its first employees. As CTO, he oversees research as well as product and workflow development at Biognosys.
Short Bio Greg Potts:
Greg Potts obtained a BSc in Chemistry from the University of Illinois Urbana-Champaign in 2011. He then earned his PhD in Chemistry from the University of Wisconsin-Madison in 2016 under the mentorship of Professor Josh Coon. Greg began his career with Thermo Fisher Scientific before joining AbbVie in the Chemical Biology and Proteomics group in 2017. His early work in industry focused on method development for MHC peptide identification and has since expanded into covalent small molecule proteome screening, mapping protein-protein interactions, and characterizing protein structural changes by MS, among other technology development projects.
Aline Martins (Scripps Research Institute)
Humans evolved under the influence of gravity, consequently, when the human body experiences weightlessness in space, many ordinary physiological functions are altered, resulting in significant phenotype changes, such as neurological impairment. We used brain organoids in space to surrogate studies in gravity-induced neural impairment on the 19th SpaceX Mission. Organoids from iPSC-derived (male patient with Rett Syndrome and his control) were grown for 35 days in the CubeLab before being returned to earth and analyzed using mass spectrometry-based proteomics. EVOSEP / timsTOF Pro 2-Bruker were the analytical tools. DIA-PASEF acquired data were processed with Spectronaut 17 (Biognosys) using both spectral library or library-free approaches (directDIA). The preliminary results suggest that microgravity induced differences in the proteome profile of some specific groups: histone deacetylation and housekeeping functions, and also in cytoskeletal and cellular structure proteins. Microgravity exerts important, neglected, and abiotic effects on neurodevelopment. MS-based proteomics can uncover the effects of microgravity in brain organoids.
Short Bio Aline Martins:
Aline Martins Graduated in Biological Sciences with a PhD in Biotechnology in the area of Functional Cancer Proteomics. Her doctoral thesis was developed in the Department of Surgery (Liver Transplantation of the University Hospital), and the experimental work was carried out at the University of Siena (UNISI) Italy. Currently, Aline works with Translational Medicine in experimental problems translated from the clinic to the benchside. Nowadays, she works at The Scripps Research Institute at Dr. John Yates’s lab developing methods using Single Cell Proteomics (SCP) that can be translated to clinics (and working with space brain organoids!!)