Sofia Emmanouela Theodorou
Analytical Scientist · Mass Spectrometry & Proteomics
Zurich, Switzerland
Specialized in high-resolution mass spectrometry-based proteomics with top training from the Aebersold (ETH Zurich) and Gygi (Harvard) labs. Expert in the end-to-end LC-MS/MS workflow, from advanced sample preparation to multi-pipeline data analysis. Currently driving small molecule analysis and chemoproteomics protocol development for covalent binder identification at Roche, with extensive experience handling complex tissue types.
Core Technical Expertise
MS Platforms
Orbitrap Exploris 480, Orbitrap Ascend, Orbitrap Eclipse, timsTOF Pro I (Bruker), Sciex QqQ (5800, 5600 QTrap), Agilent UHPLC-MS/MS, UltrafleXtreme
Techniques
DDA, DIA, PRM, diaPASEF, MRM, MALDI Imaging, HILIC-MS, UHPLC-MS/MS, microLC-MS/MS, nanoLC-MS/MS
Applications
Small molecule quantification, metabolomics, lipidomics, proteomics, biomarker discovery, covalent binder identification (ABBP), molecular toxicity assessment
Software & Analysis
SpectroMine, Skyline, Proteome Discover, vendor software (Sciex Analyst, Xcalibur), R (statistical analysis, machine learning), Excel, Python, Claude, Visual Studio Code, Git
Experience
Associate Researcher, Lead Discovery
F. Hoffmann-La Roche Ltd — Basel, Switzerland
- Performed quantification of small molecule analytes across diverse and challenging biological matrices — demonstrating proficiency in complex sample handling.
- Developed and optimized U/HPLC-MS/MS methods on several MS platforms for therapeutic target analysis.
- Developed chemoproteomics protocol to identify and characterize covalent binders in cell cultures.
- Developed microLC-HR-MS/MS methods on MS platform, optimizing DDA and PRM workflows; downstream analysis with SpectroMine, Skyline, Proteome Discover and R.
- Optimized cell culture conditions for downstream chemoproteomics assays.
- Regularly collaborated with and presented data-driven insights to senior stakeholders across project teams.
Associate Researcher, Institute of Clinical Chemistry
University Hospital of Zurich / University of Zurich — Zurich, Switzerland
- Developed HILIC-MS method on Orbitrap Exploris for evaluation of metabolic disease impact on cellular lipidome and redox potential.
- Developed UHPLC-MS/MS method on Orbitrap Exploris to monitor a novel therapeutic approach for an ophthalmic disease.
- Performed metabolomics and lipidomics data analysis on Skyline and R.
- Oversaw metabolomics and lipidomics workflows in multi-institutional collaborations.
Associate Researcher, Department of Cell Biology
Harvard Medical School — Boston, USA
- Prepared clinical samples for TMT-labeled proteomic analysis using EASY nLC and Orbitrap Exploris 480.
- Analyzed complex proteomic datasets with custom-built software; communicated findings through detailed lab reports.
- Authored, reviewed, and standardized SOPs for the core service laboratory.
- Contributed to large-scale interactome mapping project.
Assistant Researcher, Institute of Molecular Systems Biology
ETH Zurich — Zurich, Switzerland
- Developed and validated a pioneering single-cell proteomics method using bench-on-a-chip technology.
- Applied machine learning to enhance assay sensitivity in label-free proteomics studies.
- Contributed to clinical diagnostic platform for CLL patient profiling using Evosep chromatography and diaPASEF (timsTOF Pro, Bruker).
- Analyzed complex datasets in R; represented team at international conferences.
Internship, Department of Global Discovery Chemistry
Novartis Institutes for Biomedical Research — Emeryville, CA, USA
- Developed and validated qualitative and quantitative imaging mass spectrometry methods on UltrafleXtreme and Sciex 5800 (MALDI) to investigate small molecule drug molecular toxicity — including structural confirmation via exact mass and fragmentation.
- Developed HTX TM-Sprayer matrix application method; performed histology and data analysis.
- Participated in single-cell metabolomics project using Sciex 5600 QTrap; developed highly sensitive MRM method for identification and quantification of target drug and metabolites.
- Independently organized and secured funding for a scientific seminar at Stockholm University — 60+ attendees, 100% participation rate.
Education
Advanced Course: R Statistical Analysis and Visualization
Sodertorn University
MSc Analytical Chemistry
Stockholm University · ETH Zurich
Thesis: Biomarker discovery describing light-induced cellular toxicity in live cell microscopy using high-resolution mass spectrometry
Advisors: Prof. Ruedi Aebersold (ETH Zurich) & Prof. Karsten Weiss
Presented at the 2020 American Society of Mass Spectrometry international conference.
MSc Environmental Chemistry
Stockholm University
Thesis: Gene polymorphism of Glutathione-S-Transferase and acrylamide metabolism via HPLC-MS
Advisor: Prof. Margareta Torqvist
BSc Environmental Science
University of the Aegean, Greece
Erasmus+ Scholar · Recognised as the 3,000,000th European Erasmus student by the European Commission
Languages & Interests
Philosophy, contemporary dance, alpine skiing, wine and food