Sofia Theodorou

• Applying TMT quantification in proteomics and employing separation science (nLC) to study and explore changes expressed in the entire proteome associated with specific cancer or neurodegenerative diseases, leading to enhanced insights into the underlying mechanisms of these conditions. Protein ID, biomarker discovery and absolute quantification.
• Maintained and operated the mass spectrometry and HPLC instrumentation: LTQ-Orbitrap Exploris 480 and Easy nanoLC.
• Crafted precision chromatography columns, tips, and packing materials, thereby enhancing the reliability of analytical processes.
• Contributed to an industrial-scale cell culture facility, infecting 40 cultures weekly with custom-engineered viruses. Ensured rigorous sterilization protocols were followed, maintaining aseptic conditions for optimal cell growth.
• Collaborated with research groups in HMS to run proteomics experiments.
• Wrote, reviewed and improved proteomics standard operating procedures for the core service lab.

• Developed and optimized an analytical method with QqQ (Waters) to achieve separation of the glutathione analyte from the human plasma. Tested analytical columns and buffers. Developed an MRM strategy for analyte quantification, within a strict GLP-compliant environment.
• Developed an R code to conduct data analysis, focusing on identifying disparities between two instrumental methods and offering data-driven solutions.

LIMS

• Design and implement data management protocols and standards.
• Oversee the input and validation of laboratory data into the LIMS.
• Ensure data integrity, accuracy, and security.
• Customized LIMS features and modules to align with evolving laboratory needs.
• Collaborated with software developers to create custom solutions.

Supervising activities:

• Supervised and trained an intern.
• Created successful train and work schedule to maintain deadlines .
• Mentored newly hired interns on operating equipment and safety and developed training manual to use for reference.

• Developed of real single-cell proteomics analytical method using bench-on-a-chip technology.
• Analytically benchmarked (linearity, precision, accuracy and robustness) a microchip device for limited sample input down to single cell, developed for rare cancers and brain diseases.
• Assisted in the development and benchmarking of a reliable clinical diagnosis using Evosep chromatography and IM-q-TOF-diaPASEF for chronic lymphocytic leukemia patients at different stages.
• Operated and maintained an IM-q-TOF (timsTOF pro I, Bruker) and a nanoLC (nanoElute, Bruker).
• Applied a state-of-the-art statistical modeling in R and run statistical tests for targeted proteomics (TRIC for openSWATH) on large biomedical datasets, enabling evaluation of experimental procedures and identification of biomarkers.
• Managed end-to-end logistics, including budget oversight, with a weekly budget sometimes reaching up to 50,000 CHF.
• Collaborated with multiple academic institutions and industry partners in daily basis, to advance the projects.
• Developed visual content of highly complex scientific topics and represented the team at multiple conferences, showcasing our work and building relations with the academic and industrial community.

• Developed and validated qualitative and quantitative imaging mass spectrometry methods on UltraflexTreme and Sciex 5800 with MALDI source to investigate their molecular toxicity.
• Screened matrices for the imaging, developed the matrix application method HTX TM-Sprayer, sectioned with high accuracy the frozen samples, performed histologies and data analysis.
• Participated in the single cell metabolite project, that utilized a Majusima tip as the ionization source within a custom-made Sciex 5500 mass spectrometer. Identified, structurally elucidated, and successfully removed contamination, significantly enhancing the sensitivity of the method.
• Initiated, secured funding for, planned, and successfully managed a seminar at Stockholm University, with a full-house attendance of over 60 participants, achieving a commendable 100% participation rate. The seminar was followed by a well-received apéro event.