@inproceedings{GaudryHuberFlueckigeretal.2022, author = {Gaudry, Arnaud and Huber, Florian and Fl{\"u}ckiger, Julien and Quir{\´o}s, L and Rutz, Adriano and Kaiser, M and Grondin, A and Marcourt, Laurence and Ferreira Queiroz, E and Wolfender, Jean-Luc and Allard, Pierre-Marie}, title = {Short Lecture "Mass spectrometry-based sample vectorization for exploration of large chemodiverse datasets and efficient identification of new antiparasitic compounds"}, series = {Planta Medica}, volume = {88}, booktitle = {Planta Medica}, number = {15}, publisher = {Thieme}, issn = {1439-0221}, doi = {10.1055/s-0042-1758983}, year = {2022}, subject = {Massenspektrometrie}, language = {en} } @article{BittremieuxSchmidHuberetal.2022, author = {Bittremieux, Wout and Schmid, Robin and Huber, Florian and van der Hooft, Justin J. J. and Wang, Mingxun and Dorrestein, Pieter C.}, title = {Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules}, series = {Journal of the American Society for Mass Spectrometry}, volume = {33}, journal = {Journal of the American Society for Mass Spectrometry}, number = {9}, publisher = {American Chemical Society (ACS)}, issn = {1044-0305}, doi = {10.1021/jasms.2c00153}, pages = {1733 -- 1744}, year = {2022}, language = {en} } @article{deJongeMildauMeijeretal.2022, author = {de Jonge, Niek F. and Mildau, Kevin and Meijer, David and Louwen, Joris J. R. and Bueschl, Christoph and Huber, Florian and van der Hooft, Justin J. J.}, title = {Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools}, series = {Metabolomics}, volume = {18}, journal = {Metabolomics}, number = {12}, publisher = {Springer Nature}, issn = {1573-3890}, doi = {10.1007/s11306-022-01963-y}, pages = {22}, year = {2022}, abstract = {Background Untargeted metabolomics approaches based on mass spectrometry obtain comprehensive profiles of complex biological samples. However, on average only 10\% of the molecules can be annotated. This low annotation rate hampers biochemical interpretation and effective comparison of metabolomics studies. Furthermore, de novo structural characterization of mass spectral data remains a complicated and time-intensive process. Recently, the field of computational metabolomics has gained traction and novel methods have started to enable large-scale and reliable metabolite annotation. Molecular networking and machine learning-based in-silico annotation tools have been shown to greatly assist metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery. Aim of review We highlight recent advances in computational metabolite annotation workflows with a special focus on their evaluation and comparison with other tools. Whilst the progress is substantial and promising, we also argue that inconsistencies in benchmarking different tools hamper users from selecting the most appropriate and promising method for their research. We summarize benchmarking strategies of the different tools and outline several recommendations for benchmarking and comparing novel tools. Key scientific concepts of review This review focuses on recent advances in mass spectral library-based and machine learning-supported metabolite annotation workflows. We discuss large-scale library matching and analogue search, the current bloom of mass spectral similarity scores, and how molecular networking has changed the field. In addition, the potentials and challenges of machine learning-supported metabolite annotation workflows are highlighted. Overall, recent developments in computational metabolomics have started to fundamentally change metabolomics workflows, and we expect that as a community we will be able to overcome current method performance ambiguities and annotation bottlenecks.}, subject = {Metabolomik}, language = {en} } @article{GaudryHuberNothiasetal.2022, author = {Gaudry, Arnaud and Huber, Florian and Nothias, Louis-F{\´e}lix and Cretton, Sylvian and Kaiser, Marcel and Wolfender, Jean-Luc and Allard, Pierre-Marie}, title = {MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets}, series = {Frontiers in Bioinformatics}, volume = {2}, journal = {Frontiers in Bioinformatics}, publisher = {Frontiers}, issn = {2673-7647}, doi = {10.3389/fbinf.2022.842964}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-54660}, pages = {13}, year = {2022}, abstract = {In natural products research, chemodiverse extracts coming from multiple organisms are explored for novel bioactive molecules, sometimes over extended periods. Samples are usually analyzed by liquid chromatography coupled with fragmentation mass spectrometry to acquire informative mass spectral ensembles. Such data is then exploited to establish relationships among analytes or samples (e.g., via molecular networking) and annotate metabolites. However, the comparison of samples profiled in different batches is challenging with current metabolomics methods since the experimental variation—changes in chromatographical or mass spectrometric conditions - hinders the direct comparison of the profiled samples. Here we introduce MEMO—MS2 BasEd SaMple VectOrization—a method allowing to cluster large amounts of chemodiverse samples based on their LC-MS/MS profiles in a retention time agnostic manner. This method is particularly suited for heterogeneous and chemodiverse sample sets. MEMO demonstrated similar clustering performance as state-of-the-art metrics considering fragmentation spectra. More importantly, such performance was achieved without the requirement of a prior feature alignment step and in a significantly shorter computational time. MEMO thus allows the comparison of vast ensembles of samples, even when analyzed over long periods of time, and on different chromatographic or mass spectrometry platforms. This new addition to the computational metabolomics toolbox should drastically expand the scope of large-scale comparative analysis.}, subject = {Computational chemistry}, language = {en} }