GMDCSB.DB: the Golm Metabolome Database

Summary: Metabolomics, in particular gas chromatography-mass spectrometry (GC-MS) based metabolite profiling of biological extracts, is rapidly becoming one of the cornerstones of functional genomics and systems biology. Metabolite profiling has profound applications in discovering the mode of action of drugs or herbicides, and in unravelling the effect of altered gene expression on metabolism and organism performance in biotechnological applications. As such the technology needs to be available to many laboratories. For this, an open exchange of information is required, like that already achieved for transcript and protein data. One of the key-steps in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations from biological samples. Collections of mass spectra, which comprise frequently observed metabolites of either known or unknown exact chemical structure, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here we present GMD, The Golm Metabolome Database, an open access metabolome database, which should enable these processes. GMD provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds. The main goal will be the representation of an exchange platform for experimental research activities and bioinformatics to develop and improve metabolomics by multidisciplinary cooperation. Availability: http://csbdb.mpimp-golm.mpg.de/gmd.html Contact: [email protected] Supplementary information: http://csbdb.mpimp-golm.mpg.d

Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives

Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites relevant to a specific phenotypic characteristic can be identified. However, the reliability of the analytical data is a prerequisite for correct biological interpretation in metabolomics analysis. In this review the challenges in quantitative metabolomics analysis with regards to analytical as well as data preprocessing steps are discussed. Recommendations are given on how to optimize and validate comprehensive silylation-based methods from sample extraction and derivatization up to data preprocessing and how to perform quality control during metabolomics studies. The current state of method validation and data preprocessing methods used in published literature are discussed and a perspective on the future research necessary to obtain accurate quantitative data from comprehensive GC-MS data is provided

Advances in structure elucidation of small molecules using mass spectrometry

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules

A review of enhanced paramedic roles during and after hospital handover of stroke, myocardial infarction and trauma patients

BackgroundAmbulance paramedics play a critical role expediting patient access to emergency treatments. Standardised handover communication frameworks have led to improvements in accuracy and speed of information transfer but their impact upon time-critical scenarios is unclear. Patient outcomes might be improved by paramedics staying for a limited time after handover to assist with shared patient care. We aimed to categorize and synthesise data from studies describing development/extension of the ambulance-based paramedic role during and after handover for time-critical conditions (trauma, stroke and myocardial infarction).MethodsWe conducted an electronic search of published literature (Jan 1990 to Sep 2016) by applying a structured strategy to eight bibliographic databases. Two reviewers independently assessed eligible studies of paramedics, emergency medical (or ambulance) technicians that reported on the development, evaluation or implementation of (i) generic or specific structured handovers applied to trauma, stroke or myocardial infarction (MI) patients; or (ii) paramedic-initiated care processes at handover or post-handover clinical activity directly related to patient care in secondary care for trauma, stroke and MI. Eligible studies had to report changes in health outcomes.ResultsWe did not identify any studies that evaluated the health impact of an emergency ambulance paramedic intervention following arrival at hospital. A narrative review was undertaken of 36 studies shortlisted at the full text stage which reported data relevant to time-critical clinical scenarios on structured handover tools/protocols; protocols/enhanced paramedic skills to improve handover; or protocols/enhanced paramedic skills leading to a change in in-hospital transfer location. These studies reported that (i) enhanced paramedic skills (diagnosis, clinical decision making and administration of treatment) might supplement handover information; (ii) structured handover tools and feedback on handover performance can impact positively on paramedic behaviour during clinical communication; and (iii) additional roles of paramedics after arrival at hospital was limited to ‘direct transportation’ of patients to imaging/specialist care facilities.ConclusionsThere is insufficient published evidence to make a recommendation regarding condition-specific handovers or extending the ambulance paramedic role across the secondary/tertiary care threshold to improve health outcomes. However, previous studies have reported non-clinical outcomes which suggest that structured handovers and enhanced paramedic actions after hospital arrival might be beneficial for time-critical conditions and further investigation is required

Scent Marks Signal Species, Sex and Reproductive Status in Tamarins (Saguinus spp., Neotropical Primates)

Olfactory communication is an important mediator of social interactions in mammals, thought to provide information about an individual’s identity and current social, reproductive, and health status. In comparison with other taxa such as carnivores and rodents, few studies have examined primate olfactory communication. Tamarins (Callitrichidae) conspicuously deposit odorous secretions, produced by specialized scent glands, in their environment. In this study, we combined behavioral and chemical data on captive cotton-top tamarins, Saguinus oedipus, and bearded emperor tamarins, S. imperator subgrisescens, to examine the role of olfactory communication in the advertisement of species, sex, and reproductive status. We observed no difference in scent-marking behavior between species; however, females marked more frequently than males, and reproductive individuals more than non-reproductive ones. In addition, tamarins predominantly used their anogenital gland when scent-marking, followed by the suprapubic gland. We collected swabs of naturally deposited tamarin anogenital scent marks, and analyzed these samples using headspace gas chromatography-mass spectrometry. Despite a limited sample size, we established differences in tamarin anogenital mark chemical composition between species, sex and reproductive status, and identified 41 compounds. The compounds identified, many of which have been reported in previous work on mammalian semiochemistry, form targets for future bioassay studies to identify semiochemicals. Our non-invasive method for collecting deposited scent marks makes it a promising method for the study of olfactory communication in scent-marking animal species, applicable to field settings and for the study of elusive animals