| 1. |
- Heuckeroth, Steffen, et al.
(författare)
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Reproducible mass spectrometry data processing and compound annotation in MZmine 3
- 2024
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Ingår i: Nature Protocols. - : Nature Publishing Group. - 1754-2189 .- 1750-2799.
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Forskningsöversikt (refereegranskat)abstract
- Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is an open-source software for the processing of raw spectral data generated by different MS platforms. Examples include liquid chromatography-MS, gas chromatography-MS and MS-imaging. These data might typically be associated with various applications including metabolomics and lipidomics. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups: liquid chromatography-(IMS-)MS, gas chromatography-MS and (IMS-)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e., list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 h for new MZmine users and nonexperts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis.
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| 2. |
- Petroutsos, Dimitris, et al.
(författare)
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The Chloroplast Calcium Sensor CAS Is Required for Photoacclimation in Chlamydomonas reinhardtii
- 2011
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Ingår i: The Plant Cell. - : Oxford University Press. - 1040-4651 .- 1532-298X. ; 23:8, s. 2950-2963
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Tidskriftsartikel (refereegranskat)abstract
- The plant-specific calcium binding protein CAS (calcium sensor) has been localized in chloroplast thylakoid membranes of vascular plants and green algae. To elucidate the function of CAS in Chlamydomonas reinhardtii, we generated and analyzed eight independent CAS knockdown C. reinhardtii lines (cas-kd). Upon transfer to high-light (HL) growth conditions, cas-kd lines were unable to properly induce the expression of LHCSR3 protein that is crucial for nonphotochemical quenching. Prolonged exposure to HL revealed a severe light sensitivity of cas-kd lines and caused diminished activity and recovery of photosystem II (PSII). Remarkably, the induction of LHCSR3, the growth of cas-kd lines under HL, and the performance of PSII were fully rescued by increasing the calcium concentration in the growth media. Moreover, perturbing cellular Ca2+ homeostasis by application of the calmodulin antagonist W7 or the G-protein activator mastoparan impaired the induction of LHCSR3 expression in a concentration-dependent manner. Our findings demonstrate that CAS and Ca2+ are critically involved in the regulation of the HL response and particularly in the control of LHCSR3 expression.
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| 3. |
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| 4. |
- Schulte-Ladbeck, Rasmus, et al.
(författare)
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Characterization of chemical interferences in the determination of unsaturated aldehydes using aromatic hydrazine reagents and liquid chromatography
- 2001
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Ingår i: Journal of Environmental Monitoring. - : Royal Society of Chemistry. - 1464-0325 .- 1464-0333. ; 3:3, s. 306-310
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Tidskriftsartikel (refereegranskat)abstract
- A systematic investigation on interferences in the determination of unsaturated aldehydes and ketones using the 2,4-dinitrophenylhydrazine (DNPH) method is described. Acrolein, crotonaldehyde, methacrolein and 1-buten-3-one are derivatized with DNPH in the presence of an acidic catalyst to form the respective hydrazones. The unstable hydrazones react with excess reagent to form adducts. These are identified by high-performance liquid chromatography (HPLC)-mass spectrometry and spectroscopic techniques after cryogenic fraction collection of the adducts. The quantification of the unsaturated carbonyls with the DNPH method remains difficult. N-Methyl-4-hydrazino-7-nitrobenzofurazan (MNBDH) was used as an alternative reagent for this purpose. As with DNPH, the formation of a side product is observed. In contrast to DNPH, the alteration of the pH immediately after sampling leads to only one reaction product, which is stable and storable in solution at 4 degrees C for 2 days.
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| 5. |
- Thevis, Mario, et al.
(författare)
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Characterization of a non-approved selective androgen receptor modulator drug candidate sold via the Internet and identification of in vitro generated phase-I metabolites for human sports drug testing
- 2015
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Ingår i: Rapid Communications in Mass Spectrometry. - : Wiley. - 0951-4198 .- 1097-0231. ; 29:11, s. 991-999
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Tidskriftsartikel (refereegranskat)abstract
- RATIONALE: Potentially performance-enhancing agents, particularly anabolic agents, are advertised and distributed by Internet-based suppliers to a substantial extent. Among these anabolic agents, a substance referred to as LGD-4033 has been made available, comprising the core structure of a class of selective androgen receptor modulators (SARMs). METHODS: In order to provide comprehensive analytical data for doping controls, the substance was obtained and characterized by nuclear magnetic resonance spectroscopy (NMR) and liquid chromatography/electrospray ionization high resolution/high accuracy tandem mass spectrometry (LC/ESI-HRMS). Following the identification of 4-(2-(2,2,2-trifluoro-1-hydroxyethyl) pyrrolidin-1-yl)-2-(trifluoromethyl) benzonitrile, the substance was subjected to in vitro metabolism studies employing human liver microsomes and Cunninghamella elegans (C. elegans) preparations as well as electrochemical metabolism simulations. RESULTS: By means of LC/ESI-HRMS, five main phase-I metabolites were identified as products of liver microsomal preparations including three monohydroxylated and two bishydroxylated species. The two most abundant metabolites (one mono-and one bishydroxylated product) were structurally confirmed by LC/ESI-HRMS and NMR. Comparing the metabolic conversion of 4-(2-(2,2,2-trifluoro-1-hydroxyethyl) pyrrolidin-1-yl)-2-(trifluoromethyl) benzonitrile observed in human liver microsomes with C. elegans and electrochemically derived metabolites, one monohydroxylated product was found to be predominantly formed in all three methodologies. CONCLUSIONS: The implementation of the intact SARM-like compound and its presumed urinary phase-I metabolites into routine doping controls is suggested to expand and complement existing sports drug testing methods.
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