Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics.

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included

LipidBlast templates as flexible tools for creating new in-silico tandem mass spectral libraries.

Tandem mass spectral libraries (MS/MS) are usually built by acquiring experimentally measured mass spectra from chemical reference compounds. We here show the versatility of in-silico or computer generated tandem mass spectra that are directly obtained from compound structures. We use the freely available LipidBlast development software to generate 15 000 MS/MS spectra of the glucuronosyldiacylglycerol (GlcADG) lipid class, recently discovered for the first time in plants. The generation of such an in-silico MS/MS library for positive and negative ionization mode took 5 h development time, including the validation of the obtained mass spectra. Such libraries allow for high-throughput annotations of previously unknown glycolipids. The publicly available LipidBlast templates are universally applicable for the development of MS/MS libraries for novel lipid classes

Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm

BACKGROUND: Metabolomic studies are targeted at identifying and quantifying all metabolites in a given biological context. Among the tools used for metabolomic research, mass spectrometry is one of the most powerful tools. However, metabolomics by mass spectrometry always reveals a high number of unknown compounds which complicate in depth mechanistic or biochemical understanding. In principle, mass spectrometry can be utilized within strategies of de novo structure elucidation of small molecules, starting with the computation of the elemental composition of an unknown metabolite using accurate masses with errors <5 ppm (parts per million). However even with very high mass accuracy (<1 ppm) many chemically possible formulae are obtained in higher mass regions. In automatic routines an additional orthogonal filter therefore needs to be applied in order to reduce the number of potential elemental compositions. This report demonstrates the necessity of isotope abundance information by mathematical confirmation of the concept. RESULTS: High mass accuracy (<1 ppm) alone is not enough to exclude enough candidates with complex elemental compositions (C, H, N, S, O, P, and potentially F, Cl, Br and Si). Use of isotopic abundance patterns as a single further constraint removes >95% of false candidates. This orthogonal filter can condense several thousand candidates down to only a small number of molecular formulas. Example calculations for 10, 5, 3, 1 and 0.1 ppm mass accuracy are given. Corresponding software scripts can be downloaded from . A comparison of eight chemical databases revealed that PubChem and the Dictionary of Natural Products can be recommended for automatic queries using molecular formulae. CONCLUSION: More than 1.6 million molecular formulae in the range 0–500 Da were generated in an exhaustive manner under strict observation of mathematical and chemical rules. Assuming that ion species are fully resolved (either by chromatography or by high resolution mass spectrometry), we conclude that a mass spectrometer capable of 3 ppm mass accuracy and 2% error for isotopic abundance patterns outperforms mass spectrometers with less than 1 ppm mass accuracy or even hypothetical mass spectrometers with 0.1 ppm mass accuracy that do not include isotope information in the calculation of molecular formulae

An in silico MS/MS library for automatic annotation of novel FAHFA lipids.

BackgroundA new lipid class named 'fatty acid esters of hydroxyl fatty acids' (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabetes. To facilitate the automatic annotation of FAHFAs in biological specimens, a tandem mass spectra (MS/MS) library is needed. Due to the limitation of the commercial available standard compounds, we proposed building an in silico MS/MS library to extend the coverage of molecules.ResultsWe developed a computer-generated library with 3267 tandem mass spectra (MS/MS) for 1089 FAHFA species. FAHFA spectra were generated based on authentic standards with negative mode electrospray ionization and 10, 20, and 40&nbsp;V collision induced dissociation at 4 spectra/s as used in in ultra-high performance liquid chromatography-QTOF mass spectrometry studies. However, positional information of the hydroxyl group is only obtained either at lower QTOF spectra acquisition rates of 1 spectrum/s or at the MS(3) level in ion trap instruments. Therefore, an additional set of 4290 fragment-rich MS/MS spectra was created to enable distinguishing positional FAHFA isomers. The library was generated based on ion fragmentations and ion intensities of FAHFA external reference standards, developing a heuristic model for fragmentation rules and extending these rules to large swaths of computer-generated structures of FAHFAs with varying chain lengths, degrees of unsaturation and hydroxyl group positions. Subsequently, we validated the new in silico library by discovering several new FAHFA species in egg yolk, showing that this library enables high-throughput screening of FAHFA lipids in various biological matrices.ConclusionsThe developed library and templates are freely available for commercial or noncommercial use at http://fiehnlab.ucdavis.edu/staff/yanma/fahfa-lipid-library. This in silico MS/MS library allows users to annotate FAHFAs from accurate mass tandem mass spectra in an easy and fast manner with NIST MS Search or PepSearch software. The developing template is provided for advanced users to modify the parameters and export customized libraries according to their instrument features. Graphical abstractExample of experimental and in silico MS/MS spectra for FAHFA lipids

Validation Studies of the ATLAS Pixel Detector Control System

The ATLAS pixel detector consists of 1744 identical silicon pixel modules arranged in three barrel layers providing coverage for the central region, and three disk layers on either side of the primary interaction point providing coverage of the forward regions. Once deployed into the experiment, the detector will employ optical data transfer, with the requisite powering being provided by a complex system of commercial and custom-made power supplies. However, during normal performance and production tests in the laboratory, only single modules are operated and electrical readout is used. In addition, standard laboratory power supplies are used. In contrast to these normal tests, the data discussed here was obtained from a multi-module assembly which was powered and read out using production items: the optical data path, the final design power supply system using close to final services, and the Detector Control System (DCS). To demonstrate the functionality of the pixel detector system a stepwise transition was made from the normal laboratory readout and power supply systems to the ones foreseen for the experiment, with validation of the data obtained at each transition.Comment: 8 pages, 8 figures, proceedings for the Pixel2005 worksho

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.

In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hits, showing that the use of in silico methods is still important

Gebäudebegrünung zur Vorbeugung und Minderung von Klimafolgen

Die zunehmende Häufung extremer Wetterereignisse wie Hitzeperioden, Dürren oder Starkregen stellt Städte vor Herausforderungen. Trotz zahlreicher, bereits umgesetzter Klimaschutz- und -anpassungsmaßnahmen besteht die Notwendigkeit, sich noch stärker auf die bereits eingetretenen und insbesondere auf die zukünftig projizierten Folgen einzustellen. Neben einer klimaangepassten Stadtplanung und einem Ausbau der sogenannten grünen Infrastruktur durch Grünflächen und Parks bildet die Bepflanzung von Dächern und Fassaden eine wichtige Option. Technisch wird danach differenziert, ob das Wurzelwerk im Boden oder an der Fassade selbst verankert ist, ob die Bepflanzung eine Kletterhilfe benötigt oder ob sie modular als Flächenkonstruktion angebracht wird. Die Gebäudebegrünung bietet sich in verdichteten Stadtgebieten besonders an, da sie keinen oder nur wenig zusätzlichen Platz verbraucht. Die mit einer Bauwerksbegrünung verbundenen Erwartungen richten sich auf eine Minderung von Hitzeinseleffekten, eine bessere Rückhaltung von Regenwasser nach Starkregenereignissen, eine Erhöhung der Luftqualität und überdies auf einen Beitrag zur Erhöhung der städtischen Biodiversität. Während der mögliche Nutzen mit Blick auf die Energieeffizienz auf Gebäudeebene schon intensiv untersucht ist, liegen Erkenntnisse zu Kosten-Nutzen-Berechnungen und Effekten für das Stadtklima wegen der bislang geringen Verbreitung großflächiger Gebäudebegrünungen bisher nur auf Basis von Pilotansätzen und Simulationen vor. Zudem sind schwierig zu bewertende Nutzenaspekte, wie die Förderung der Biodiversität und die Reduktion des Hitzeinseleffektes in Städten, noch wenig erfasst. Herausforderungen und gleichzeitig Potenziale ergeben sich aus der kombinierten Nutzung der für Begrünung nutzbaren Flächen mit Solaranlagen, da einerseits Flächenkonkurrenz besteht, anderseits Synergien aufgrund einer gesteigerten Energieeffizienz der Solaranlagen genutzt werden können. Neben weiteren Forschungsbedarfen liegt die größte Herausforderung für die Gebäudebegrünung vor allem in ihrer tatsächlichen Umsetzung. Eine deutliche Steigerung der Begrünungsmaßnahmen könnte durch geeignete Anreizstrukturen und Erleichterungen bei der Nutzung bestehender Fördermöglichkeiten erreicht werden

Beschränkung von Liveveranstaltungen während der ­Coronapandemie – ökonomische Auswirkungen und digitale Lösungen im Kulturbetrieb

Die Coronapandemie stellt alle Bereiche der Gesellschaft vor große Herausforderungen. Besonders hart trifft sie Kulturschaffende und Kultureinrichtungen aus der Musik- und Filmwirtschaft sowie den darstellenden Künsten, weil öffentliche Veranstaltungen bzw. Liveevents, die eine maßgebliche Umsatzquelle darstellen, in Phasen des Lockdowns nicht durchgeführt werden können und sonst, wenn überhaupt, nur unter hohen Hygieneauflagen möglich sind. Digitale Technologien können eine Chance bieten, alternative Einnahmequellen zu generieren, um die aktuellen Umsatzeinbußen auszugleichen. Die Kulturwirtschaft setzt sich schon seit Jahren mit dem Thema Digitalisierung auseinander. Museen beispielsweise digitalisieren und virtualisieren ihre Ausstellungsstücke. Angebote sind etwa virtuelle Rundgänge über die kommerzielle Plattform von Google Art & Culture oder Smartphoneanwendungen mit Zusatzinformationen (Guides). Schwieriger ist es jedoch für die Bereiche Musik und Film sowie die darstellenden Künste. Theater, Opernhäuser, Konzerte, Klubs oder Kinos leben von der physischen Präsenz des Publikums, wenngleich es bereits schon vor der Pandemie einige digitale Nischenangebote gab, etwa die Online Concert Hall der Berliner Philharmonie oder Streamingangebote der New York Metropolitan Opera. Im Zuge der Coronakrise erproben immer mehr Akteure, ihre bisherigen Liveveranstaltungen als digitale Angebote zu präsentieren und zu vermarkten. Dazu wurden beispielsweise Konzerte und Aufführungen vor leeren Sälen gespielt und online übertragen. Viele dieser Angebote sind jedoch kostenlos oder setzen auf Spenden als Einnahmequelle. Eine bislang offene Frage ist, wie langfristig profitable Geschäftsmodelle aussehen könnten, die auf digitalen Lösungen aufbauen

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains