10 0.35


0.30 0.25 0.20 0.15 0.10 0.05


0.00 0 50 100 150 200 250


Figure 5: Substructure annotation for transformation product HO-PEG6-CH2COOH. Substructure annotation is directly visualised in SIRIUS.


Conclusion


SIRIUS offers a comprehensive approach to assessing pharmaceutical contamination by combining precursor drug screening and transformation product screening.


SIRIUS is not limited to public chemical databases, but can be used effectively to search custom databases of structure candidates generated, for example, by tools such as BioTransformer. Additionally, SIRIUS provides multiple validation levels, including spectral library searches, confi dence scores for database hits, and substructure annotations (see Figure 5) for a more in-depth investigation of results.


The ability to screen transformation products without requiring reference spectra is particularly valuable not only for pharmaceuticals but also for pesticides and industrial chemicals, whose degradation products may have significant environmental impacts.


Additional Resources


Learn more about the method: https://bright-giant.com/labmate-transformation-products Download SIRIUS: https://bright-giant.com/labmate-sirius-release-latest


Notes


1 Available online as LUXPHARMA (S76) on Zenodo (DOI: 10.5281/zenodo.4587356) 2


MassBank-data release 2024.11 (DOI: 10.5281/zenodo.14221628) 3 LC-MS/MS Spectra from https://mona.fi ehnlab.ucdavis.edu/downloads


4


For metabolism prediction we chose AllHuman, which predicts small molecule metabolism in the human superorganism. It covers biotransformations occurring


300 m/z


substructure annotations for transformation product HO-PEG6-CH2COOH


both in human tissues as well as the gut microbiota. We predict 3 steps. https:// biotransformer.ca/help


5


The biomolecule structure database is an aggregation of several structure databases containing small molecules of biological interest, including metabolites and other compounds of biological relevance, natural products, synthetic products with potential bioactivity, and contaminants observed in experiments. https://v6.docs.sirius-ms.io/ methods-background/#CSIFingerID


Differences in identifi cation numbers compared to the study by Singh et al.1 may be attributed to our approach of excluding the precursor peak during spectral matching.


6


A confi dence score threshold of 0.64 roughly corresponds to FDR 10 % in evaluations (Hoffmann et al. 2022)


7 8


Dimethyl phthalate’s production and use as a plasticizer for nitrocellulose and cellulose acetate, resins, rubber, and in solid rocket propellants; in lacquers; plastics; rubber; coating agents; safety glass and in molding powders (Lewis 2007) may result in its release to the environment through various waste streams(SRC). https://pubchem.ncbi.nlm.nih.gov/compound/8554


References


Djoumbou-Feunang, Yannick, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach, and David S. Wishart. 2019. ‘BioTransformer: A Comprehensive Computational Tool for Small Molecule Metabolism Prediction and Metabolite Identifi cation’. Journal of Cheminformatics 11 (1): 2.


Dührkop, Kai, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V. Melnik, Marvin Meusel, Pieter C. Dorrestein, Juho Rousu, and Sebastian Böcker. 2019. ‘SIRIUS 4: A Rapid Tool for Turning Tandem Mass Spectra into Metabolite Structure Information’. Nature Methods 16 (4): 299–302.


Dührkop, Kai, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. 2015. ‘Searching Molecular Structure Databases with Tandem Mass Spectra Using CSI:FingerID’. Proceedings of the National Academy of Sciences of the United States of America 112 (41): 12580–85.


Hoffmann, Martin A., Louis-Félix Nothias, Marcus Ludwig, Markus Fleischauer, Emily C. Gentry, Michael Witting, Pieter C. Dorrestein, Kai Dührkop, and Sebastian Böcker. 2022. ‘High-Confidence Structural Annotation of Metabolites Absent from Spectral Libraries’. Nature Biotechnology 40 (3): 411–21.


Lewis, Richard J. Sr 2007. Hawley’s Condensed Chemical Dictionary, Book and CD-ROM Set. Wiley-Interscience.


Singh, Randolph R., Adelene Lai, Jessy Krier, Todor Kondić, Philippe Diderich, and Emma L. Schymanski. 2021. ‘Occurrence and Distribution of Pharmaceuticals and Their Transformation Products in Luxembourgish Surface Waters’. ACS Environmental Au 1 (1): 58–70.


Wishart, David S., Siyang Tian, Dana Allen, Eponine Oler, Harrison Peters, Vicki W. Lui, Vasuk Gautam, Yannick Djoumbou-Feunang, Russell Greiner, and Thomas O. Metz. 2022. ‘BioTransformer 3.0-a Web Server for Accurately Predicting Metabolic Transformation Products’. Nucleic Acids Research 50 (W1): W115–23.


Read, Share and Comment on this Article, visit: www.labmate-online.com New spectroscopy products available following company relocation


Following its relocation to a new headquarters west of Stuttgart, Maassen GmbH has expanded its product portfolio, enhancing manufacturing and distribution capabilities. The new facility enables increased production of proprietary and additional products, supporting a broader range of customer needs.


Press production continues, with ongoing expansion of available press tool diameters. The company also offers hard metal (KXF tungsten carbide/cobalt mixture) press plates in various sizes.


In addition to its existing range of products for ICP-OES, ICP-MS, AAS, and UV-VIS spectrometers from renowned manufacturers such as GlassExpansion and Burgener Research, Maassen GmbH has partnered with MeiHui Technology Japan / UVTech to supply high-quality light source modules. This includes deuterium lamps from Hamamatsu Photonics, socketed by MeiHui Technology for spectrometers from leading manufacturers. These light sources will be stocked in Europe in the coming months.


With this expansion, Maassen GmbH can now provide light sources for a wider range of spectrometers and HPLC systems. Customer testing has confi rmed fi tting accuracy and compatibility with various manufacturers’ equipment, while Hamamatsu Photonics’ long-life lamps have demonstrated consistent quality over the years.


A website relaunch is in progress, but inquiries about new products can be made via email. More information online: ilmt.co/PL/5O34


63766pr@reply-direct.com Ultrafast fi bre laser enables supercontinuum generation


Chromacity Ltd reports that the outstanding coupling effi ciency and high stability of its Model 1040 ultrafast fi bre laser enable the generation of exceptionally broad and fl at supercontinua in the near-infrared region (750-1300 nm).


This compact and user-friendly laser provides an ideal solution for producing a cost-effective near-infrared supercontinuum by focusing ultrashort pulses into nonlinear materials, such as photonic crystal fi bres. Unlike solid-state lasers, which typically produce beams with an elliptical cross- section, the Model 1040 laser outputs from a single-mode fi bre, ensuring a perfectly symmetric beam that achieves coupling effi ciencies exceeding 75% into photonic crystal fi bres.


A technical note from Chromacity explores the implementation of supercontinuum generation in nonlinear fi bres as a cost-effective method for producing broadband near-infrared light. This light source is well-suited for applications such as spectroscopy, optical coherence tomography, and CARS spectroscopy/microscopy.


To access the technical note, visit ilmt.co/PL/z5Vz. The Model 1040 is a fi xed-wavelength femtosecond laser source that delivers ultrashort pulses with high average powers in the near-infrared region.


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INTERNATIONAL LABMATE - APRIL 2025


relative intensity


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