Ayesha Chaudhry
Brampton,ON
Summary
Bioanalytical Scientist with expertise in mass spectrometry, protein chemistry, and method development. Skilled in LC-MS/MS, HDX-MS, recombinant protein workflows, and biophysical characterization, with experience developing robust quantitative assays in both academic and clinical settings. Proficient in experimental design, instrumentation troubleshooting, and advanced data analysis using DynamX, MassLynx, PLGS, DriftScope, PyMOL, and Schrodinger. Strong collaborator and communicator, adept at translating complex data into actionable insights for high-impact research and method development projects.
Overview
5
5
years of professional experience
Work History
Graduate Assistant
York University
09.2021 - Current
- Operated, maintained, and troubleshot advanced LC-MS and ion mobility mass spectrometry platforms (Waters SYNAPT G2, cyclic ion mobility MS, and SCIEX ZenoTOF 7600), ensuring optimal instrument performance, data quality, and minimal downtime.
- Designed, optimized, and supported protein-focused LC-MS workflows, including conventional and sub-second HDX-MS, to investigate protein conformation and dynamics in structured and intrinsically disordered proteins, from experimental design through data analysis.
- Developed and optimized HPLC separation methods (SEC, RP, IEX), including sample preparation, cleanup, and desalting strategies for protein and peptide analyses.
- Performed in-house recombinant protein expression in bacterial systems, utilizing GST-tag and/or IMAC affinity purification to generate high-purity protein samples for downstream MS, and biophysical studies.
- Conducted comprehensive biophysical and structural characterization of biologics using intact MS, SDS-PAGE, BLI, SEC-HPLC, and UV-Vis spectroscopy to assess protein identity, purity, stability, aggregation, and higher-order structure.
- Processed, analyzed, and interpreted complex MS datasets using DynamX, PLGS, MassLynx, Mass Spec Studio, DriftScope, UniDec, PyMOL, Deuteros, PeakView, and related software, delivering reproducible and interpretable results.
- Collaborated effectively in interdisciplinary research teams, contributing analytical expertise to method development, data interpretation, and cross-functional problem-solving.
- Demonstrated strong scientific communication skills through peer-reviewed publications, conference presentations, and clear technical reporting.
- Planned and executed assay optimization and documentation independently, while supporting effective knowledge transfer within collaborative research programs, and meeting project timelines.
Teaching Assistant
York University
09.2021 - Current
- Demonstrated and guided complex laboratory experiments, ensuring safety, accuracy, and reproducibility.
- Assisted in experiment setup, reagent preparation, and instrument calibration for undergraduate labs.
- Evaluated lab reports, quizzes, and exams, providing detailed feedback, and fostering analytical skills.
- Mentored students individually and in groups, enhancing problem-solving skills and independent lab techniques.
- Collaborated with faculty to optimize lab workflows and maintain organized, well-equipped laboratory environments.
Research Intern
DYNACARE
06.2025 - 08.2025
- Led the development and analytical validation of quantitative LC-MS/MS protein assays in biological matrices, establishing foundational proteomics workflows for future clinical diagnostic applications in alignment with ISO/IEC 17025 accreditation.
- Designed and optimized a generic protein digestion workflow, systematically evaluating protein denaturation strategies, proteolytic enzymes, and digestion kits to improve digestion efficiency, reproducibility, and quantitative performance.
- Developed and implemented desalting and sample cleanup protocols to minimize matrix effects and salt interference, improving LC-MS robustness for serum-based proteomics assays.
- Designed, optimized, and qualified liquid chromatography methods using SCIEX Exion LC platform to ensure peptide separation, assessing column chemistries, mobile phases, flow rates, and temperature conditions to ensure consistent assay performance.
- Built and optimized MRM-based LC-MS/MS methods on SCIEX x500 for quantitative analysis of protein standards (e.g., albumin), and translated these workflows toward clinical biomarker applications.
- Developed an LC-MS/MS clinical assay for thyroglobulin quantification in human serum, supporting post-thyroidectomy monitoring for residual or metastatic thyroid tissue.
- Contributed to data analysis (SCIEX OS, Analyst and MS Office), method documentation, SOP development, and quality assurance activities, supporting compliant assay implementation within a regulated clinical laboratory environment.
- Applied GLP-compliant practices in handling human samples, operating analytical instrumentation, and maintaining traceable experimental records.
Research Assistant
Explorer Research
11.2020 - 06.2021
- Designed and executed behavioral experiments to investigate consumer responses, using advanced instrumentation, including eye-tracking, EEG, VR, and facial coding.
- Collected and analyzed large, complex datasets using quantitative and qualitative methods to identify patterns and actionable insights.
- Maintained experimental protocols, ensured data integrity, and optimized equipment performance for reproducible results.
- Collaborated with multidisciplinary teams to interpret data and communicate technical findings clearly to stakeholders.
Education
Ph.D. - Chemistry
York University
Toronto, ON08.2026
Master of Science - Chemistry
York University
Toronto, ON05.2022
Bachelor of Science (Honors) - Biochemistry
York University
Toronto, ON12.2020
Skills
- Mass spectrometry and chromatography: LC-MS/MS, ion mobility MS, HDX-MS, MRM, HPLC (SEC, RP, IEX)
- Protein and biophysical techniques: recombinant protein expression, GST/IMAC purification, SDS-PAGE, BLI, SEC-HPLC, UV-Vis spectroscopy, NMR (industrial-focused training)
- Data analysis and software: AutoDock Vina, PyMOL, Schrodinger, Waters DynamX, PLGS, MassLynx, DriftScope, MS Studio, Microsoft Office
- Experimental design and workflow optimization: Assay development, protein digestion, desalting, buffer exchange, instrument calibration, and troubleshooting
- Quality and collaboration: GLP, ISO/IEC 17025, SOPs, QA/QC, data integrity, cross-functional teamwork, technical reporting
Publications
- “Apparatus for Automated Continuous Hydrogen Deuterium Exchange Mass Spectrometry Measurements from Milliseconds to Hours” (Analytical Chemistry)
- "The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain" (Protein Science)
- "Millisecond Hydrogen Deuterium Exchange for Characterization of Weak Binding Interactions and Disordered Conformational Dynamics" (Protein Science - under review)
- “Conformational Dynamics of the STAT5B SH2 Domain in the Wild-Type vs. a Constitutively Activated Mutants” (In preparation)
- “Mapping the Conformational Landscape of Hyperphosphorylated Tau using millisecond HDX-MS” (In preparation)
Timeline
Research Intern
DYNACARE
06.2025 - 08.2025
Graduate Assistant
York University
09.2021 - Current
Teaching Assistant
York University
09.2021 - Current
Research Assistant
Explorer Research
11.2020 - 06.2021
Ph.D. - Chemistry
York University
Master of Science - Chemistry
York University
Bachelor of Science (Honors) - Biochemistry
York University