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Directory and Skills inventory

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Miladinovic Sasa

Miladinovic Sasa

Professeur-e HES Associé-e

Main skills

Mass spectrometry

Proteomics

Metabolomics

Bioanalysis

AI/ML tools

Liquid chromatography

Small molecule analysis

Highlights

Publications
Green analytical chemistry: integrating sustainability into undergraduate education
Research
AIM-MS: AI-driven LC-MS for Biopharmaceutical Analysis
Research
Discovery of early-stage biomarkers for a periodontitis point-of-care diagnostic
  • Contact

  • Teaching

  • Research

  • Publications

  • Conferences

Main contract

Professeur-e HES Associé-e

Desktop: ENP.19.N506

HES-SO Valais-Wallis - Haute Ecole d'Ingénierie
Rue de l'Industrie 23, 1950 Sion, CH
HEI - VS
Faculty
Chimie et sciences de la vie
Main Degree Programme
Ingénierie des Sciences du vivant

Saša M. Miladinović received his Ph.D. in analytical chemistry from the University of Arkansas (USA) under the supervision of Professor Charles L. Wilkins, working on high-resolution mass spectrometry of synthetic polymers. He then held postdoctoral fellowships at EPFL Lausanne in the laboratory of Professor Yury Tsybin, on high-resolution top-down mass spectrometry of intact proteins and peptides, and at ETH Zürich with Professor Ruedi Aebersold, on targeted and untargeted quantitative proteomics.

After several years in industry as a research scientist, developing quantitative LC-MS bioanalytical methods for small molecules, pharmaceuticals and proteins including monoclonal antibodies, he returned to academia. He is now Associate Professor of Bioanalytical Chemistry at HES-SO Valais/Wallis, where he leads the Mass Spectrometry and Separation Sciences Laboratory (MS³L).

He teaches mass spectrometry, separation science, structural elucidation, green analytical chemistry and proteomics at bachelor level, and bioanalysis in regulated environments and LC-MS proteomics for biomarker discovery at master level. He supervises bachelor each year. 

Research: Mass Spectrometry and Separation Sciences Laboratory (MS³L)

MS³L develops and applies high-resolution quantitative mass spectrometry coupled to advanced separation techniques, addressing analytical challenges in biological, food, environmental and industrial samples. The group combines robust instrumentation with AI- and machine learning-based data processing; work currently supported by an Innosuisse grant.

Research topics:

  • AI/ML-driven workflows for mass spectrometry data processing and method development
  • Biopharmaceutical characterization and quantification
  • Quantitative and qualitative proteomics and metabolomics
  • Biomarker discovery
  • Bioanalysis (e.g. antibiotics)
  • Mycotoxin extraction and analysis in food
  • Environmental contaminant screening (PFAS)

The group works across analytical chemistry and data science, develops scalable and reproducible methods, trains the next generation of analytical scientists, and collaborates with partners in academia, industry and the public sector.

BSc HES-SO en Ingénierie des sciences du vivant - HES-SO Valais-Wallis - Haute Ecole d'Ingénierie
  • Mass spectrometry
  • Green analytical chemistry
  • Bioanalytical lab
  • Structure identification
  • Liquid chromatography lab
  • Advanced bioanalysis
MSc HES-SO en Life Sciences - HES-SO Master
  • Biomarkers
  • Bioanalytics in a regulated environment

Ongoing

Discovery of early-stage biomarkers for a periodontitis point-of-care diagnostic

Role: Main Applicant

Financement: Innocheque

Description du projet:

We aim to identify biomarkers of periodontitis while in an early and still revisible phase by developing a LC-MS metabolomics workflow specifically for gingival crevicular fluid and applying it to longitudinal samples. The results will lay the foundations for a future point-of-care diagnostic test.

Research team within HES-SO: Miladinovic Sasa

Partenaires professionnels: Oesterle Ian, Scafra Gmbh

State: Ongoing

AIM-MS: AI-driven LC-MS for Biopharmaceutical Analysis

Role: Main Applicant

Financement: Innosuisse

Description du projet:

The AIM-MS project aims to develop and deliver to Genedata AG, a Swiss bioinformatics company, a dedicated software platform built around self-learning, AI-driven mechanisms. The platform is designed to simplify and automate the process of data analysis for LC-MS workflows.

Research team within HES-SO: Miladinovic Sasa , Mermoud Grégory

Partenaires professionnels: Ossola Reto, Genedata

State: Ongoing

Horizon Europe - Scaling-up nutritional proteins from alternative sources

Role: Co-applicant

Description du projet:

  • Demonstrate innovative processes for the extraction and/or production of proteins for application as nutritional food, starting from alternative sources. 
  • Address efficient and cost-effective downstream separation and purification processes (when applicable), to meet the targeted quality and stability for final applications.
  • Demonstrate nutritional adequacy of the targeted product(s) and their effect on food formulation(s) according to established testing procedures.
  • Address resource efficiency and circularity aspects to increase economic and socio-environmental added value. 
  • Test the safety of developed proteins and formulations through toxicological tests, in line with EU regulatory requirements and EFSA guidelines. Moreover, identify potential regulatory gaps and provide recommendations to overcome potential bottlenecks.
  • Include a task on consumer awareness and acceptance: involve end-users (including consumers) starting from the early stages to assess market acceptance of the novel proteins and incorporate insights in product development.
  • Ensure complementarities with past and ongoing R&I projects addressing similar challenges, including projects funded under Horizon 2020 / Horizon Europe and by the BBI JU / CBE JU.

Research team within HES-SO: Miladinovic Sasa

Partenaires académiques: TU Delft

Partenaires professionnels: ADAMO FOODS LTD

State: Ongoing

2026

Urinary volatilomics for biomarker discovery in kidney stone patients and healthy controls
Scientific paper

Pascal Fuchsmann, Eugenia Pertziger, Hélène Y. Meng, Miladinovic Sasa, Murielle Bochud, Carsten A. Wagner, Olivier Bonny, Guy Vergères

Urolithiasis, 2026 , vol.  54, no  137, pp.  1-15

Link to the publication

2025

Quantitation of antibiotics in fresh fermentation medium by hydrophilic interaction chromatography mass spectrometry
Scientific paper ArODES

Nadia Marcon, Mathias Rüdt, Joachim Klein, Sasa Miladinovic

Analytical and bioanalytical chemistry,  2025, 417, 9, 1927-1934

Link to the publication

Summary:

This study presents the development of a sophisticated liquid chromatography-mass spectrometry approach leveraging hydrophilic interaction chromatography (HILIC) for the quantification of kanamycin and spectinomycin in fermentation media. The method was validated per International Council for Harmonisation guidelines, demonstrating robust linearity, precision, and accuracy. To mitigate pronounced matrix effects common to complex fermentation matrices, sample preparation was thoroughly optimized with solid-phase extraction employing MCX sorbent, thereby enhancing recovery rates and minimizing analytical interference. The validated protocol demonstrated high correlation coefficients (R > 0.998), underscoring its robustness and reliability for the accurate quantification of antibiotics in challenging bioprocess environments, providing a valuable analytical tool for bioreactor system monitoring.

Quantitation of antibiotics in fresh fermentation medium by hydrophilic interaction chromatography mass spectrometry
Scientific paper

Marcon Nadia, Rüdt Matthias, Joachim Klein, Miladinovic Sasa

Analytical and Bioanalytical Chemistry, 2025 , pp.  1-8

Green analytical chemistry: integrating sustainability into undergraduate education
Scientific paper

Miladinovic Sasa

Analytical and Bioanalytical Chemistry, 2025

Link to the publication

2024

Localization of disulfide bonds in ribonuclease using low pH trypsin and LC-ESI-QTOF-MS
Scientific paper ArODES

Amélie Bornex, Sasa Miladinovic

CHIMIA,  2024, 78, 12, 881-882

Link to the publication

Summary:

We evaluated a method to localize disulfide bonds in bovine pancreatic ribonuclease (RNase) by applying low pH trypsin protein digestion with a bottom-up LC-ESI-QTOF-MS approach. The goal was to minimize disulfide bond scrambling during sample preparation. By using N-ethylmaleimide (NEM) for alkylation of free cysteines, we achieved 92% sequence coverage and successfully identified the native disulfide bonds between specific cysteine residues. However, scrambled disulfide bonds were also observed. Our results indicate that while this low pH digestion method helps preserve native disulfide bonds, further refinement is needed to fully prevent disulfide bond rearrangement during sample preparation.

Green analytical chemistry : integrating sustainability into undergraduate education
Scientific paper ArODES

Sasa Miladinovic

Analytical and Bioanalytical Chemistry,  2024, 417, 4, 665-673

Link to the publication

Localization of Disulfide Bonds in Ribonuclease Using Low pH Trypsin and LC-ESI-QTOF-MS
Scientific paper

Amélie Bornex, Miladinovic Sasa

CHIMIA, 2024

Link to the publication

2023

Mycotoxin Recovery and Matrix Effect in Fava Bean Starch and Protein Isolate Measured by LC-MS/MS
Scientific paper

Miladinovic Sasa

CHIMIA, 2023

Link to the publication

2022

Chemical, Analytical and Pharmacokinetic Characterisation of RO7304898, an API Consisting of Two Rapidly Interconverting Diastereoisomers
Scientific paper

Katja Heinig, Filippo Sladojevich, Jeannine Schaffland, Georg Jaeschke, Alfred Ross, Philipp Koldewey, Miladinovic Sasa, Jin Wang, Caroline Rynn

Pharmaceutical Research, 2022

Link to the publication

Impact of charge patches on tumor disposition and biodistribution of therapeutic antibodies
Scientific paper

Jakob Stüber, Karin Rechberger, Miladinovic Sasa, Thomas Pöschinger, Tamara Zimmermann, Remi Villenave, Miro Eigenmann, Thomas Kraft, Dhaval Shah, Hubert Kettenberger, Wolfgang Richter

AAPS open, 2022

Link to the publication

2015

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues*[s]
Scientific paper

Roland Bruderer, Oliver Bernhardt, Tejas Gandhi, Miladinovic Sasa, Lin-Yang Cheng, Simon Messner, Tobias Ehrenberger, Vito Zanotelli, Yulia Butscheid, Claudia Escher, Olga Vitek, Oliver Rinner, Lukas Reiter

Molecular & Cellular Proteomics, 2015

Link to the publication

2014

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
Scientific paper

Hannes Röst, George Rosenberger, Pedro Navarro, Ludovic Gillet, Miladinovic Sasa, Olga Schubert, Witold Wolski, Ben Collins, Johan Malmström, Lars Malmström, Ruedi Aebersold

Nature biotechnology, 2014

Link to the publication

2012

In-spray supercharging of peptides and proteins in electrospray ionization mass spectrometry
Scientific paper

Miladinovic Sasa, Luca Fornelli, Yu Lu, Krzysztof Piech, Hubert Girault, Yury Tsybin

Analytical chemistry, 2012

Link to the publication

2008

Developments in MALDI Mass Spectrometry: The Quest for the Perfect Matrix
Scientific paper

Mariccor Batoy, Evgenia Akhmetova, Miladinovic Sasa, Joseph Smeal, Charles Wilkins

Applied Spectroscopy Reviews, 2008

Link to the publication

2026

A Green and Robust ASE–LC–MS/MS Strategy for Multianalyte Mycotoxin Determination in Plant Protein Isolate
Conference

Miladinovic Sasa, Marcon Nadia, Romain Gabioud, Emie Scheidegger

26th International Mass Spectrometry Conference, 22.08.2026 - 28.08.2026, Lyon, France

Link to the conference

Towards Greener Extraction of Mycotoxins from Protein Concentrates for LC–MS/MS Analysis
Conference

Miladinovic Sasa

6th International Conference on Green Chemistry and Renewable Energy, 18.06.2026 - 20.06.2026, Barcelona, Spain

2025

Advanced quantitative LC-MS analysis of mycotoxins in plant-based protein isolates
Conference

Miladinovic Sasa

ANAKON 2025, 10.03.2025 - 13.03.2025, Leipzig, Germany

Link to the conference

2024

Quantitative LC-MS analysis of mycotoxins in plant-based protein isolates Oral presentation
Conference

Miladinovic Sasa

8th MS in food DAYS, 16.10.2024 - 18.10.2024, Brindisi, Italy

Link to the conference

2023

Liquid Chromatography/Mass Spectrometry Analysis of Proteins: Fundamentals and Applications
Conference

Miladinovic Sasa

Euroanalysis 2023, 27.08.2023 - 31.08.2023, Geneve

Link to the conference

LC-MS Analysis of Antibiotics in Fermentation Medium Invited talk
Conference

Miladinovic Sasa

Euroanalysis 2023, 27.08.2023 - 31.08.2023, Geneva

Link to the conference

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