EMU: Acquisition of an upgrade for a liquid chromatography system coupled to a mass spectrometer to improve the range of analyses performed at the REDOX PROTEOMICS CORE, a Multiuser Proteomics Laboratory at IQ / USP.

• Grant number: 23/17031-8
• Support Opportunities: Research Infrastructure Program - Small Medium Sized
• Start date: September 01, 2024
• End date: August 31, 2027
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Graziella Eliza Ronsein
• Grantee: Graziella Eliza Ronsein
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Danilo Bilches Medinas ; Deborah Schechtman

Abstract

Since 2016, the REDOX PROTEOMICS CORE, a multi-user laboratory associated with the Analytical Center of the Institute of Chemistry / USP, has been offering specialized proteomic analysis to users from the State of São Paulo, from other states and even internationally. This proposal requests an upgrade to the instrumentation dedicated to proteomic analyses available in REDOX PROTEOMICS CORE. The upgrade includes the following accessories: 1) Multifunctional LC system; 2) FAIMS Pro Duo Interface for ion mobility 3) Internal ion source EASY-ETD (Electron-Transfer Dissociation). The requested upgrade will provide considerable improvements in three main areas: 1) increase in sample processing capacity; 2) increase in the number of peptide and protein identifications in each sample, combined with a decrease in chemical noise and matrix effects; 3) Adding a new capacity to the facility - identifying post-translational modifications. Currently, one of the major bottlenecks for our facility is the high demand/waiting time for analyses. Our mass spectrometer operates 24 hours a day, 7 days a week. Still, the waiting list for sample injection is approximately 2 months. The replacement of the current nanoLC system (which has since been discontinued by the company) with a more modern system, in addition to providing more options for chromatographic separation, will provide a saving of approximately 30% in analysis time for each sample. This time saving is key, especially for projects involving cohort studies. In parallel, the acquisition of the "FAIMS Pro" ion mobility interface will add a new separation modality to the peptides, orthogonal to the separation that occurs during elution by the chromatographic column. This orthogonal selectivity introduced by the FAIMS interface excludes ions derived from contaminants and system noise, increasing sensitivity and the limits of detection and quantification. Ion mobility is a tool that allows the identification and quantification of proteins present in very low abundance in extremely complex samples, composed of non-protein matrices and/or with large amounts of contaminants. Examples are feces, brain tissue and tissues fixed with formalin in paraffin. Finally, by incorporating the ability to fragment by ETD, we will offer for the users of the REDOX PROTEOMICS CORE the state of the art in the analysis of post-translational modifications. Research that focuses on cell signaling would benefit enormously from incorporating ETD into our platform. Another area that would be especially benefited from the acquisition of the internal ETD source is the study of the REDOX proteome, especially with regard to cysteine residues and disulfide bonds. This is a central area of study for several users of the facility. It is estimated that with the update of the equipment already available in our centralized multi-user laboratory, which includes more advanced options, and at the frontier of knowledge in proteomics, the REDOX PROTEOMICS CORE will be able to provide proteomic analyses for São Paulo state, with the same quality of the results obtained in renowned international centers of excellence. (AU)