Translational Mass Spectrometry and Biomarker Research

PD Dr. Patrick Öckl

Areas of investigation/research focus

Diagnosis of neurodegenerative diseases and monitoring of disease progression is mainly based on clinical symptoms. This is hampered by the symptomatic overlap between some neurodegenerative diseases bearing the risk of misdiagnosis. In addition, early diagnosis in the asymptomatic stage is impossible.

A biomarker is “a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention (National Institutes of Health, NIH)”. It can help to improve differential and early diagnosis and monitor and predict disease progression. Biomarkers are also essential for the evaluation of treatment effects in clinical trials. The measurement of biomarkers in biological fluids such as blood or cerebrospinal fluid (CSF) is an established procedure and used in clinical routine for many diseases. However, only few reliable biomarkers in blood or CSF are available so far for neurodegenerative diseases.

Our group focuses on the discovery of novel and the detailed characterization of existing fluid biomarkers (proteins/peptides) for neurodegenerative diseases especially for amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). We use different mass spectrometric approaches and immunoassays (ELISA, Simoa, Ella) to measure biomarkers in clinical samples (CSF, serum, plasma), tissue and preclinical samples in the context of a translational research strategy (in collaboration with other DZNE groups in Ulm).

Mass spectrometry (MS) coupled with liquid chromatography (LC-MS/MS) offers the possibility to measure several thousand proteins in a single sample (untargeted/shotgun proteomics) and is ideally suited to study changes of protein abundance in ALS/FTLD patients and uncover disease-related mechanisms and biomarker candidates. We successfully applied MS in the past to identify novel biomarker candidates in CSF for ALS/FTLD such as UCHL1, MAP2, GPNMB or NPTXR which are now characterized in more detail. A special focus of this DZNE cooperation unit is the study of peptides and their alterations in ALS/FTLD (peptidomics).

Targeted MS, i.e. the measurement of a selected number of biomarkers by MS, is a possibility to use highly specific MS for measurement of large sample numbers and can be an alternative to immunoassays for biomarker validation. We develop targeted MS approaches (MRM, PRM) for the validation of biomarker candidates from proteomic/peptidomic studies in large patient cohorts in case immunoassays are not available or unreliable.

Examples of targeted MS assays which have been successfully developed or implemented in our lab are the measurement of:

  1. Beta-Synuclein by IP-MS in blood (marker of synaptic degeneration in Alzheimer´s disease, Oeckl et al., JPR 2020)
  2. Abeta42/40 by IP-MS in blood (marker of amyloid pathology in Alzheimer´s disease)
  3. Synucleins (alpha/beta/gamma) by MRM in CSF (markers of synaptic degeneration, Oeckl et al., MCP 2016)
  4. Ubiquitin by MRM in CSF (Oeckl et al., JPR 2014)
  5. VGF by MRM in CSF (synaptic marker, van Steenoven et al., IJMS 2019)

We are equipped with state-of-the-art technology to perform biomarker research and studies in clinical samples:

Mass Spectrometry

  1. Thermo Exploris 480 Orbitrap with FAIMS-Pro interface and Ultimate 3000 RSLCnano LC
  2. Sciex QTRAP6500 with MicroLC200 and Agilent 1260
  3. Thermo Q Exactive Orbitrap with Ultimate 3000 RSLCnano LC


  1. Quanterix Simoa HD-1 analyzer
  2. ProteinSimple Ella system

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