is Stephan Müller Version 3

Senior expert in biopharmaceutical mass spectrometry 

Former head of central Mass Spectroscopy facility, then of a section for project analytics (GC, LC, MS, NMR) in Roche’s innovation center in Basel. 30 years of experience in pioneering MS and LC/MS applications for drug discovery including related IT projects. Founder and owner of GmbH aimed at facilitating access of discovery scientists to external analytical resources and expertise. 

Lecturer at the school of pharmacy at the University of Basel, on analytical technologies and applications in pharma research. See my lecture subsite.

more on LinkedIn – contact me under

Pioneer achievements of our team at Roche

Extensive small molecule biomarker experience

Biological mass spectrometry

  • Introduction of biophysical MS methods at Roche (with and by A.Topp): Affinity selection mass spectrometry (ASMS) and native mass spectrometry of soluble and membrane proteins
  • Establishment of in-house metabolic biomarker facility to supply target engagement data for discovery biology using LC/MS, GC/MS and NMR (with V. Stierlin, I. Ruf, M. Wittig, A. Stämpfli, C. Tournoux, A.Topp, B.Bürgi)
  • Re-establishment of NMR and LC/MS based metabolomics capability for biomarker discovery in (stem) cell cultures (A. Stämpfli, A. Ross) to discover metabolism reactions to genomic change and markers for phenotypic screening
  • Introduction of MS readouts for bioassays at Roche Basel –  automation and introduction of a LC/MS based drug-drug interaction assay from Roche Nutley, assays for enzyme inhibitors for cerebrosides, steroids, lipids, (with I. Ruf) multienzyme profiling readout for the optimization of an ultraselective steroid synthesis inhibitor (with M. Wittig)
  • Development of stable isotope tracer applications e.g. for the determination of biosynthesis rates of cholesterol or glucose (with V. Stierlin, C. Albrecht, M. Wittig)

Chemistry support

  • Introduction of LC/MS compound quality control hand-in-hand with narrow bore NMR and complete informatics workflow including structure display and structure based automatic ESI-MS and UV signal prediction (with C.Albrecht)


  • Establishment of rapid metabolite identification service for discovery projects (I. Ruf)
  • Introduction of LC/MS rodent DMPK analysis for infectious disease discovery, including cassette dosing experiments (C. Albrecht, V. Stierlin, I. Ruf)


  • IT: Development and introduction of several LIMS systems, automated data analysis systems for LC/MS bioanalysis and compound quality control with integration of corporate structure database (With G. Schmitt), design and maintenance of department website. 


Plasma, serum, cerebrospinal fluid (CSF), bronchoalveolar lavage fluid (BALF), aqueous humor, vitreous humor (ophtalmology), brain, liver, muscle, kidney tissue, cell cultures and stem cell derived differentiated cells (e.g. neurons)


Dopamin and metabolites (catecholamines), histamin and metabolites, trace amines, GABA and metabolites, sphingolipids and cerebrosides, neurosteroidal stress hormones, amino acids, nucleosides and nucleotides

Cardiovascular and metabolic diseases

Fatty acids, neutral sterols, steroids (extensive), carnitine and acylcarnitines, phosphatidyl-, lysophosphatidyl cholines and -acids, S1P, glucose and gluconeogenesis intermediates including stable isotope tracer studies, cholesterol biosynthesis intermediates including stable isotope tracer studies, eicosanoids. 

Vitamin research

Stable isotope study on enantioselective PK of Tocopherol diastereomers, hydroxy-nonenal as oxidative stress biomarker


see metabolic

Infectious diseases

Pseudomonas specific metabolites (pyocyanins and analogs), nucleosides and nucleotides


Amino acids and metabolites

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