CASE via MS: Ranking Structure Candidates by Mass Spectra

Two important tasks in computer-aided structure elucidation (CASE) are the generation of candidate structures from a given molecular formula, and the ranking of structure candidates according to compatibility with an experimental spectrum. Candidate ranking with respect to electron impact mass spectra is based on virtual fragmentation of a candidate structure and comparison of the fragments’ isotope distributions against the spectrum of the unknown compound, whence a structure–spectrum compatibility matchvalue is computed. Of special interest is the matchvalue’s ability to distinguish between the correct and false constitutional isomers. Therefore a quality score was computed in the following way: For a (randomly selected) spectrum–structure pair from the NIST MS library all constitutional isomers are generated using the structure generator MOLGEN. For each isomer the matchvalue with respect to the library spectrum is calculated, and isomers are ranked according to their matchvalues. The quality of the ranking can be quantified in terms of the correct structure’s relative ranking position (RRP). This procedure was repeated for 100 randomly selected spectrum–structure pairs belonging to small organic compounds. In this first approach the RRP of the correct isomer was 0.27 on average

Computational Exploration of the Chemical Space Surrounding the Molecules of Life

How the transition of disorganized, inanimate matter to organized, living systems took place on our planet and might have occurred on other bodies of our solar system or elsewhere in the universe is one of the fundamental questions studied in the field of astrobiology. The only instance of life known so far is the terrestrial one, and all living organisms on Earth share many of the same biochemical foundations with respect to reproduction and metabolism. These biochemical foundations rely on a small pool of biomolecules, which represent a minute subset of plausible structural analogs, which themselves form only a very small fraction of all possible chemical compounds in chemical space. We believe that one key to understanding the origins of life is to study biomolecules in the context of their surrounding neighborhood in chemical space. Using unique software tools, so-called structure generators, we are able to exhaustively construct well defined subsets of chemical space. These virtual compound libraries are then computationally analyzed with respect to the physico-chemical properties of their constituents. In this talk some basic mathematical models and computational aspects of generating molecular structures are presented, results concerning the amino acid alphabet, nucleotide analogs and the core of intermediary metabolism are summarized, and perspectives of ongoing studies related to astrobiology exploration missions are outlined

Atmospheric methane with SCIAMACHY: Operational Level 2 data analysis and verification

SCIAMACHY is a passive imaging spectrometer mounted on board ESA’s ENVISAT satellite to probe a large number of atmospheric trace gas species, such as methane, and their global distribution and evolution. Methane (CH4) is particularly interesting as it is one of the most abundant greenhouse gas in the Earth atmosphere. To analyze SCIAMACHY methane measurements, we used the DLR BIRRA (Beer InfraRed Retrieval Algorithm) to retrieve nadir methane concentrations from its infrared spectra in channel 6. By integrating the DLR BIRRA code into ESAs operational Level 2 processor, we expanded it to include atmospheric CH4 column measurements. We have therefore performed an extensive test and verification operation. Our tests are based on separate comparisons with existing space and ground-based obtained measurements of methane column density. We present here our strategy for quality check of this first version of a CH4 product. We will further discuss specific geographical areas we used to validate the products

The Post-COVID-19 Era: Interdisciplinary Demands of Contagion Surveillance Mass Spectrometry for Future Pandemics

Mass spectrometry (MS) can become a potentially useful instrument type for aerosol, droplet and fomite (ADF) contagion surveillance in pandemic outbreaks, such as the ongoing SARS-CoV-2 pandemic. However, this will require development of detection protocols and purposing of instrumentation for in situ environmental contagion surveillance. These approaches include: (1) enhancing biomarker detection by pattern recognition and machine learning; (2) the need for investigating viral degradation induced by environmental factors; (3) representing viral molecular data with multidimensional data transforms, such as van Krevelen diagrams, that can be repurposed to detect viable viruses in environmental samples; and (4) absorbing engineering attributes for developing contagion surveillance MS from those used for astrobiology and chemical, biological, radiological, nuclear (CBRN) monitoring applications. Widespread deployment of such an MS-based contagion surveillance could help identify hot zones, create containment perimeters around them and assist in preventing the endemic-to-pandemic progression of contagious diseases

New Developments in the SCIAMACHY Level 2 Ground Processor Towards Version 7

SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric ChartographY) aboard ESA’s environmental satellite ENVISAT observed the Earth’s atmosphere in limb, nadir, and solar/lunar occultation geometries covering the UV-Visible to NIR spectral range. It is a joint project of Germany, the Netherlands and Belgium and was launched in February 2002. SCIAMACHY doubled its originally planned in-orbit lifetime of five years before the communication to ENVISAT was severed in April 2012, and the mission entered its post-operational phase. In order to preserve the best quality of the outstanding data recorded by SCIAMACHY, data processors are still being updated. This presentation will highlight three new developments that are currently being incorporated into the forthcoming Version 7 of ESA’s operational Level 2 processor: 1. Tropospheric BrO, a new retrieval based on the scientific algorithm of (Theys et al., 2011). This algorithm had originally been developed for the GOME-2 sensor and was later adapted for SCIAMACHY. 2. Improved cloud flagging using limb measurements (Liebing, 2015). Limb cloud flags are already part of the SCIAMACHY L2 product. They are currently calculated employing the scientific algorithm developed by (Eichmann et al., 2015). Clouds are categorized into four types: water, ice, polar stratospheric and noctilucent clouds. High atmospheric aerosol loadings, however, often lead to spurious cloud flags, when aerosols had been misidentified as clouds. The new algorithm will better discriminate between aerosol and clouds. It will also have a higher sensitivity w.r.t. thin clouds. 3. A new, future-proof file format for the level 2 product based on NetCDF. The data format will be aligned and harmonized with other missions, particularly GOME and Sentinels. The final concept for the new format is still under discussion within the SCIAMACHY Quality Working Group

Life-Detection Technologies for the Next Two Decades

Since its inception six decades ago, astrobiology has diversified immensely to encompass several scientific questions including the origin and evolution of Terran life, the organic chemical composition of extraterrestrial objects, and the concept of habitability, among others. The detection of life beyond Earth forms the main goal of astrobiology, and a significant one for space exploration in general. This goal has galvanized and connected with other critical areas of investigation such as the analysis of meteorites and early Earth geological and biological systems, materials gathered by sample-return space missions, laboratory and computer simulations of extraterrestrial and early Earth environmental chemistry, astronomical remote sensing, and in-situ space exploration missions. Lately, scattered efforts are being undertaken towards the R&D of the novel and as-yet-space-unproven life-detection technologies capable of obtaining unambiguous evidence of extraterrestrial life, even if it is significantly different from Terran life. As the suite of space-proven payloads improves in breadth and sensitivity, this is an apt time to examine the progress and future of life-detection technologies.Comment: 6 pages, the white paper was submitted to and cited by the National Academy of Sciences in support of the Astrobiology Science Strategy for the Search for Life in the Univers

SCIAMACHY: The new Level 0-1 Processor

SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) is a scanning nadir and limb spectrometer covering the wavelength range from 212 nm to 2386 nm in 8 channels. It is a joint project of Germany, the Netherlands and Belgium and was launched in February 2002 on the ENVISAT platform. After the platform failure in April 2012, SCIAMACHY is now in the postprocessing phase F. SCIAMACHY�s originally specified in-orbit lifetime was double the planned lifetime. SCIAMACHY was designed to measure column densities and vertical profiles of trace gas species in the mesosphere, in the stratosphere and in the troposphere (Bovensmann et al., 1999). It can detect a large amount of atmospheric gases (e.g. O3 , H2CO, CHOCHO, SO2 , BrO, OClO, NO2 , H2O, CO, CH4 , among others ) and can provide information about aerosols and clouds. The operational processing of SCIAMACHY is split into Level 0-1 processing (essentially providing calibrated radiances) and Level 1-2 processing providing geophysical products. The operational Level 0-1 processor has been completely re-coded and embedded in a newly developed framework that speeds up processing considerably. In the frame of the SCIAMACHY Quality Working Group activities, ESA is continuing the improvement of the archived data sets. Currently Version 9 of the Level 0-1 processor is being implemented. It will include An updated degradation correction Several improvements in the SWIR spectral range like a better dark correction, an improved dead & bad pixel characterisation and an improved spectral calibration Improvements to the polarisation correction algorithm Improvements to the geolocation by a better pointing characterisation Additionally a new format for the Level 1b and Level 1c will be implemented. The version 9 products will be available in netCDF version 4 that is aligned with the formats of the GOME -1 and Sentinel missions. We will present the first results of the new Level 0-1 processing in this paper

An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions

A central question in origins of life research is how non-entailed chemical processes, which simply dissipate chemical energy because they can do so due to immediate reaction kinetics and thermodynamics, enabled the origin of highly-entailed ones, in which concatenated kinetically and thermodynamically favorable processes enhanced some processes over others. Some degree of molecular complexity likely had to be supplied by environmental processes to produce entailed self-replicating processes. The origin of entailment, therefore, must connect to fundamental chemistry that builds molecular complexity. We present here an open-source chemoinformatic workflow to model abiological chemistry to discover such entailment. This pipeline automates generation of chemical reaction networks and their analysis to discover novel compounds and autocatalytic processes. We demonstrate this pipeline's capabilities against a well-studied model system by vetting it against experimental data. This workflow can enable rapid identification of products of complex chemistries and their underlying synthetic relationships to help identify autocatalysis, and potentially self-organization, in such systems. The algorithms used in this study are open-source and reconfigurable by other user-developed workflows

VirES for Aeolus, a Virtual Workspace for ESA's Atmospheric Dynamics Mission

VirES is a Virtual workspace for Earth-observation Scientists, a service provided by the European Space Agency (ESA). VirES has firstly been established for ESA's magnetic field mission Swarm as "VirES for Swarm" and has been extended to ESA's atmospheric dynamics mission Aeolus, which is scheduled for launch in August 2018. The service is developed by the Austrian IT company EOX in strong collaboration with missions' scientists. VirES is a web-based service (https://vires.services) that enables scientists to discover, visualize, select and download data of Earth-observation missions through an easy to operate graphical user interface. "VirES for Aeolus" will provide access to Aeolus L1B, L2A, L2B, L2C products and auxiliary data. The first version 1.0 passed acceptance tests in April 2018 and developments towards Version 1.1 (launch version) are in progress. The service is planned to be accessible for public use as soon as the mission's commissioning phase is completed and first data products are released by ESA

SCIAMACHY: Level 0-1 Processor V9 and Phase F Re-processing

SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) is a scanning nadir and limb spectrometer covering the wavelength range from 212 nm to 2386 nm in 8 channels. It is a joint project of Germany, the Netherlands and Belgium and was launched in February 2002 on the ENVISAT platform. After the platform failure in April 2012, SCIAMACHY is now in the postprocessing phase F. Its originally specified in-orbit lifetime was double the planned lifetime. SCIAMACHY was designed to measure column densities and vertical profiles of trace gas species in the mesosphere, in the stratosphere and in the troposphere (Bovensmann et al., 1999). It can detect a large amount of atmospheric gases (e.g. O3 , H2CO, CHOCHO, SO2 , BrO, OClO, NO2 , H2O, CO, CH4 , among others ) and can provide information about aerosols and clouds. The operational processing of SCIAMACHY is split into Level 0-1 processing (essentially providing calibrated radiances) and Level 1-2 processing providing geophysical products. The operational Level 0-1 processor has been completely re-coded and embedded in a newly developed framework that speeds up processing considerably. In the frame of the SCIAMACHY Quality Working Group activities, ESA is continuing the improvement of the archived data sets. Version 9 of the Level 0-1 processor includes - An updated degradation correction - Improvements to the polarisation correction algorithm - Improvements to the geolocation by a better pointing characterisation - Several improvements in the SWIR spectral range like a better dark correction, an improved dead & bad pixel characterisation and an improved spectral calibration The new format for the Level 1b and Level 1c will be netCDF V4. We will present the verification results and the results of the mission re-processing