SGMS School: Best practices in small molecules analysis
Detection and identification of small molecules from complex mixtures using GC- and LC-MS is like looking for a needle in a haystack. This 3rd SGMS school is intended for participant with basic knowledge of mass spectrometry. Strategies and tools will be presented that enable data processing with confident authentication, structure elucidation, and quantification. The relevance of improved annotations will be illustrated by presentations from different applied areas including e.g. food safety, and water contaminants. Aspects of quality control and assessment of compound properties in drug discovery used in pharmaceutical industry will also be treated. The second day will be focussed on best practices in metabolomics and lipidomics, including analytical methods, data processing, and the use of metabolic pathways in the annotation.
Small Molecules Metabolomics & Lipidomics
Abstracts Small Molecules Abstracts Metabolomics & Lipidomics
The 2021 SGMS School is about best practices and current challenges in small molecule analysis with modern mass spectrometry. The objectives are to exchange and review the best practices to analysis of small molecules (metabolites), including experimental and data processing/analysis approaches.
Detection and identification of small molecules from complex mixtures using GC- and LC-MS is like looking for a needle in a haystack. This 3rd SGMS school is intended for participants with basic knowledge of mass spectrometry. Strategies and tools will be presented that enable data processing with confident authentication, structure elucidation, and quantification. The relevance of improved annotations will be illustrated by presentations from different applied areas including e.g. food safety, water contaminants, and metabolomics. Aspects of quality control and assessment of compound properties in drug discovery used in pharmaceutical industry will also be treated. The second day will be focused on best practices in metabolomics and lipidomics, including analytical methods, data processing, and the use of metabolic pathways in the annotation.
The workshop is designed for the academic and industrial analytical departments, with a focus on industrial scientists, advanced graduate students, post-docs and scientists in the areas of analytical chemistry, synthetic organic chemistry, physical chemistry, biochemistry and biotechnology.
Format & program
The program is built around didactic lectures and practical workshops, with a particular emphasis on hands-on problem solving, obtaining practical knowledge of data processing, and interaction with the faculty. The 2021 SGMS School will take place in a in an on-site format. A valid COVID-certificate is needed for participation.
Registration information (on the homepage of the SGMS 2021 meeting)
Small molecules
Plenary sessions
- Anton Kaufmann (Kantonales Labor Zürich)
- Participating in small molecule proficiency tests with HRMS; a bold decision?
- Andreas Topp (Roche)
- Turn the light towards small molecules in the drug discovery process
Lessons
- Bertran Rubi (ETH Zurich)
- Best practice in mass spectrometry: The sample and the selection of the best ionization method
- Maurus Biedermann (Kantonales Labor Zürich)
- Analysis of complex mixtures by GCxGC-MS, food contaminates as an example
- Silvan Eichenberger (Lonza)
- Mass Spectrometry @ LONZA Visp: Insights into daily business of quality control
- Heinz Singer (Eawag)
- Identification of organic contaminants in water samples – LC-HRMS analysis and workflow
Exercise sessions
- Laurent Bigler (University of Zurich) & Yuri Tsybin (Spectroswiss)
- Fundamentals in MS (isotopic distribution, resolution, mass accuracy, chemical forms)
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- Open-access web browser tools for annotation of complex mass spectra, contaminants, polymers, and isotopic enrichment
Abstracts Plenary sessions (small molecules)
Participating in small molecule proficiency tests with HRMS; a bold decision?
Anton Kaufmann (Kantonales Labor Zürich)
Laboratories working in the field of small molecule residue analysis (e.g. pesticides, veterinary drugs and environmental contaminants) in complex matrices are required to regularly participate in proficiency tests (PT) to prove their capability of detecting and accurately quantifying residues of interest. Routine residue analysis is still overwhelmingly dominated by tandem quadrupole instrumentation (QqQ) which has been termed the “gold standard”. Considering the importance of receiving good PT scores, is it wise to analyse an unknown PT sample with HRMS, while dozens of other participating laboratories use their time proven QqQ instrumentation? This question shall be answered by comparing the outcomes of the more than 100 different PT tests in which we have participated during a period of nearly 10 years.
Turn the light towards small molecules in the drug discovery process
Andreas Topp (Roche)
The drug discovery process focuses on many different target classes and is addressed by many different modalities like large molecules (antibodies), RNA or Small Molecules. Within this lecture an overview on Mass Spec based methods and tasks in small molecule drug discovery processes is provided. This will including in vivo target engagement (e.g. small molecule biomarker analyses) through biochemical assays (e.g. assay development, HTS, Cpd.profiling) and ends up with biophysical Mass Spec methods (direct and indirect binding assays).
Metabolomics & lipidomics
Plenary sessions
- Serge Rudaz & Victor Gonzalez-Ruiz (University of Geneva)
- Metabolomics best practice - Overview
- Jean-Luc Wolfender (University of Geneva)
- Solutions for annotating metabolites without reference spectra with the highest possible confidence
Lessons
- Hector Gallart-Ayala (UNIL)
- Lipidomics workflow - from data acquisition, raw data to annotated lipid data sets
- Michael Witting (Helmholtz Centre Munich)
- GNPS ecosystem use case
- Ralf Weber (Phenome Center Birmingham)
- Deep annotation of model organisms
Exercise sessions
- Endre Laczko (Functional Genomics Centre Zurich)
- Metabolomics/lipidomics data set analysis and interpretation using MetaboAnalyst
- Ralf Weber (Phenome Center Birmingham)
- Data mining (Deepen the lessen 'Deep annotatin of model organisms', focus advanced annotation approaches)
Abstracts Plenary sessions (metabolomics & lipidomics)
Metabolomics best practice - Overview
Serge Rudaz & Victor Gonzalez-Ruiz (University of Geneva)
As untargeted metabolomic methodologies are becoming increasingly used in various fields, several trusted good practices are being identified and widely accepted within the community. Such practices span from the experimental design downstream to the interpretation of the results, including quality assurance (QA) and quality control (QC) to ensure the reliability of the obtained results. In this workshop, best practices in untargeted metabolomics will be covered, providing an overview of the most widely used procedures, their strengths and limitations, and a practical insight into how they can be implemented in research laboratories.
Solutions for annotating metabolites without reference spectra with the highest possible confidence
Jean-Luc Wolfender (University of Geneva)
The identification of metabolites in metabolomics remains a major challenge. In bioactive natural product research more than 300,000 compounds have been described today. As there is no really centralised database of reference spectra, except for a few model organisms, accurate annotation of a given natural product in an extract is difficult. In order to overcome these limitations, we are using approaches of annotation on GNPS. We combine this with searches against in silico MS/MS spectra over a wide range of structures. We also integrate taxonomic information to refine the structure predictions. This allows the structural class of metabolites to be determined with a high degree of confidence and gives the possibility to document the composition of organisms of interest as accurately as possible. Practical examples of this approach and a discussion of the possibilities and limitations will be given.