Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard, since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for nonpeptidic analytes.

Two new furoquinoline alkaloids, maculine B (1) and kokusaginine B (2) and one new dihydrooxazole alkaloid, veprisazole (3), along with four known compounds namely, N13-methyl-3-methoxyrutaecarpine (4), flindersiamine (5), skimmianine (6) and tilianin (7) were isolated from the methanol extract of the stem bark of Araliopsis soyauxii Engl. by various chromatographic methods. Their structures were determined using spectrometry and spectroscopic techniques including NMR and MS. The cytotoxicity of the new compounds compared to that of doxorubicin, the reference anticancer compound, was determined on a panel of nine cancer cell lines including sensitive and drug resistant phenotypes. The three previously undescribed alkaloids displayed selective activities. Maculine B (1), the most active one among the newly described compounds, exhibited IC50 below 30 μM against CCRF-CEM leukemia and U87MG glioblastoma cells.

Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.

Metabolic fingerprinting is a powerful analytical technique, giving access to high-throughput identification and relative quantification of multiple metabolites. Because of short analysis times, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is the preferred instrumental platform for fingerprinting, although its power in analysis of free fatty acids (FFAs) is limited. However, these metabolites are the biomarkers of human pathologies and indicators of food quality. Hence, a high-throughput method for their fingerprinting is required. Therefore, here we propose a MALDI-TOF-MS method for identification and relative quantification of FFAs in biological samples of different origins. Our approach relies on formation of monomolecular Langmuir films (LFs) at the interphase of aqueous barium acetate solution, supplemented with low amounts of 2,5-dihydroxybenzoic acid, and hexane extracts of biological samples. This resulted in detection limits of 10–13–10–14 mol and overall method linear dynamic range of at least 4 orders of magnitude with accuracy and precision within 2 and 17%, respectively. The method precision was verified with eight sample series of different taxonomies, which indicates a universal applicability of our approach. Thereby, 31 and 22 FFA signals were annotated by exact mass and identified by tandem MS, respectively. Among 20 FFAs identified in Fucus algae, 14 could be confirmed by gas chromatography-mass spectrometry.

Twenty compounds were isolated from the hydroethanolic extract of the stems of Siolmatra brasiliensis, five flavonoids, two lignans, one glucosyl phytosterol, seven nor-cucurbitacins, one new phenolic derivative named siolmatrin (1) and four new dammarane-type saponins named siolmatrosides II-V (2–5), the structures of the compounds were assigned by means of 1D and 2D NMR experiments and HRESIMS of the natural compounds and some acetyl derivatives. The effects of the crude hydroethanolic extract (SbExt) and the ethyl acetate fraction (SbEtAc) of Siolmatra brasiliensis stems on the formation of advanced glycation end-products (AGEs) were also investigated. In the in vitro model system of protein glycation using bovine serum albumin (BSA) and glucose, addition of SbExt or SbEtAc inhibited the formation of fluorescent AGEs, in parallel to minor levels of fructosamine (SbEtAc) and markers of tyrosine and tryptophan oxidation (SbExt and SbEtAc). Protein crosslinking, which represents changes of late stages of protein glycation, was reduced in the presence of SbExt and SbEtAc. Siolmatra brasiliensis stems seem to be a promising source of compounds having ability to prevent glycoxidation changes, arising as an interesting option to be studied as a complementary therapy for complications of diabetes.

In the search for bioactive natural products from the African flora, three previously undescribed compounds including one stilbene-coumarin derivative (1), one coumarin-carbinol (2) and one fatty glycoside (3) were isolated from the stem bark and leaves of Monotes kerstingii, together with sixteen known compounds (4–19). The structures of the isolated compounds were elucidated based on their NMR and MS spectroscopic data and by comparison of these data with those previously reported in the literature. Compounds 1–19 were screened for anthelmintic and antimicrobial activity. None of the compounds exhibited significant anthelmintic activity. However, compounds 4, 5, 8 and 14 displayed interesting antibacterial activity against B. subtilis at a concentration of 100 μM with respective inhibition percentages of 99, 79, 71 and 100%, respectively, compared to erythromycin used as positive control. In addition, at the same concentration, compound 6 showed remarkable antifungal activity against Septoria tritici with 93.6% growth inhibition and was found to be more active than the positive controls epoconazole and terbinafine displaying 76.6 and 84.3%, respectively.

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

Pyrofomins A-D, four polyoxygenated sesquiterpenoids have been isolated from the methanolic extract of the fruit bodies of Pyrofomes demidoffii. Their structures are elucidated by IR, HR-FTICR-MS, and 2D NMR spectroscopy. Furthermore, the cedrane carbon skeleton of pyrofomin A (1) is confirmed by X-ray crystallographic analysis. The sesquiterpenoids 1–4 show neither cytotoxicity against KB cells nor antimicrobial activity.

The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS1 abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application “MetFamily”, which is freely available at http://msbi.ipb-halle.de/MetFamily/. MetFamily provides a dynamic link between the patterns based on MS1-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS1 patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR.

A new dihydroflavonol–flavonol biflavonoid derivative, named ericoside was isolated from the ethanol extract of the whole plant of Erica mannii along with the known flavonoid, taxifolin 3-O-α-l-rhamnopyranoside; and two readily available sterols (sitosterol, sitosterol 3-O-β-d-glucopyranoside). The isolation was performed using chromatographic methods and the structure of purified molecules were elucidated using spectroscopic techniques (e.g. MS, NMR) and by comparison with literature data. The crude ethanol extract, ericoside, and taxifolin 3-O-α-l-rhamnopyranoside were tested against ten Gram-negative bacteria including multidrug resistant clinical isolates using a broth microdilution method. The crude ethanol extract showed no noteworthy activity. Of the purified compounds, ericoside displayed moderate activity against the resistant Escherichia coli AG100 with a MIC of 64 μg/mL.