Non-target screening with high-resolution mass spectrometry: critical review using a collaborative trial on water analysis

In this article, a dataset from a collaborative nontarget screening trial organised by the NORMAN Association is used to review the state-of-the-art and discuss future perspectives of non-target screening using high-resolution mass spectrometry in water analysis. A total of 18 institutes from 12 European countries analysed an extract of the same water sample collected from the River Danube with either one or both of liquid and gas chromatography coupled with mass spectrometry detection. This article focuses mainly on the use of high resolution screening techniques with target, suspect, and non-target workflows to identify substances in environmental samples. Specific examples are given to emphasise major challenges including isobaric and co-eluting substances, dependence on target and suspect lists, formula assignment, the use of retention information, and the confidence of identification. Approaches and methods applicable to unit resolution data are also discussed. Although most substances were identified using high resolution data with target and suspect-screening approaches, some participants proposed tentative non-target identifications. This comprehensive dataset revealed that nontarget analytical techniques are already substantially harmonised between the participants, but the data processing remains time-consuming. Although the objective of a Bfullyautomated identification workflow^ remains elusive in the short term, important steps in this direction have been taken, exemplified by the growing popularity of suspect screening approaches. Major recommendations to improve non-target screening include better integration and connection of desired features into software packages, the exchange of target and suspect lists, and the contribution of more spectra from standard substances into (openly accessible) databases.This work was supported in part by the SOLUTIONS project, which received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under Grant Agreement No. 603437

RNomics: a computational search for box C/D snoRNA genes in the D. melanogaster genome.

Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome. Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. Availability: Additional information is available at http://www. bioinformatica.unito.it/bioinformatics/snoRNA

Actual contamination of the Danube and Sava Rivers at Belgrade (2013)

This study was focussed on a comprehensive investigation on the state of pollution of the Danube and Sava Rivers in the region of Belgrade. Different complementary analytical approaches were employed covering both i) organic contaminants in the river water by target analyses of hormones and neonicotinoids as well as non-target screening analyses and ii) heavy metals in the sediments. Finally, some common water quality parameters were analysed. The overall state of pollution is on a moderate level. Bulk parameters did not reveal any unusual observations. Moreover, quantification of preselected organic contaminants did not indicate to elevated pollution. More significant contaminations were registered for chromium, nickel, zinc and partially copper in sediments with values above the target values according to Serbian regulations. Lastly, non-target screening analysis revealed a wider spectrum of organic contaminants comprising pharmaceuticals, technical additives, personal care products and pesticides. The study presented a comprehensive view on the state of pollution of the Sava and Danube Rivers and is the base for setting up further monitoring programs. As a superior outcome, it was illustrated how different chemical analyses can result in different assessments of the river quality. A comparison of target and non-target analyses pointed to potential misinterpretation of the real state of pollution

Why do the poor leave the safety net in Mexico? A study of the effects of conditionality on dropouts

This paper analyzes the characteristics of beneficiaries that drop out of the Mexican conditional cash transfer program Oportunidades to determine if dropping out of the program is a result of selftargeting by the non-poor, the exclusion of the target poor population or a combination of both. The analysis, which uses a duration model, indicates that it is the wealthier beneficiaries that have greater odds of dropping out suggesting that conditionality acts as a screening device. Results also indicate that administrative factors and the particular provider of health services to beneficiaries have an important influence on dropouts.Cash transfer programs, conditionality, Oportunidades, Latin America, Mexico, hazard models

Risk Factors, Knowledge, and Beliefs about Cervical Cancer Screening and Screening Practices among Appalachian Women

Background: A priority of the National Cancer Institute and Centers for Disease Control and Prevention includes research to promote cervical cancer screening in diverse populations based on socioeconomic status, race and ethnicity. Poor white population in rural Appalachia have greater cancer burden and resemble other minority populations such as African Americans and Hispanics (Friedell, Linville, & Hullet, 1998). Cervical cancer screening has greatly decreased mortality in the United States overall, but screening rates remain lower and mortality rates are higher within the population of Appalachian women (Freidel et al., 1992 & Hall, Uhler, Coughlin, & Miller, 2002). Objectives: The purposes of this study were to examine the relationships between: 1) knowledge and beliefs regarding cervical cancer screening and actual screening practices; and 2) risk factors of smoking and alcohol use and actual screening practices in a cohort of Appalachian women. Method: A secondary analysis was performed using data from a larger study conducted among non-Amish women residing in two Appalachian counties in Ohio. The target population for the primary study was women residing in Appalachian Ohio. All women completed a one hour health-related questionnaire conducted by trained interviewers. The secondary analysis examined those data that pertained to cervical cancer screening practices, smoking history, and alcohol use. Knowledge and belief-related barriers about cervical cancer screening were also described. Results: Results were analyzed using descriptive statistics and Chi-square tests. The sample size included 89 eligible participants whose mean age was 58 years (SD=15.3) with a mean education of 12.7 years (SD=2.1). Most women (59%) indicated having employer paid health insurance. In the past year, 72% of the women did not have a pap smear, or cervical cancer screening. Cost of screening was not significantly related to being screened (χ2 = 0.33, df= 1, p=0.56). Twelve percent of women were current smokers, 32% were former smokers, and 56% were never smokers. Chi-square analysis found no correlation between the women having received pap smears within the last year and their smoking status (χ2 =1.25, df= 2, p=0.53). In the past year, 15.7% of the women reported binge drinking. Although not significant, Chi-square analysis indicated a trend for non-binge drinking women to be less likely to have had a pap test (χ2 = 2.97, df= 1, p=0.085). Similarly, there was a trend for between current smoking and binge drinking (χ2 = 4.87, df= 2, p= 0.088). Almost all, or 92% of participants were knowledgeable about cervical cancer screening tests. Knowledge deficit items affected 14.6% of women, and 11% indicated beliefs which acted as barriers to screening

Antitubercular specific activity of ibuprofen and the other 2-arylpropanoic acids using the HT-SPOTi whole-cell phenotypic assay

Objectives: Lead antituberculosis (anti-TB) molecules with novel mechanisms of action are urgently required to fuel the anti-TB drug discovery pipeline. The aim of this study was to validate the use of the high-throughput spot culture growth inhibition (HT-SPOTi) assay for screening libraries of compounds against Mycobacterium tuberculosis and to study the inhibitory effect of ibuprofen (IBP) and the other 2-arylpropanoic acids on the growth inhibition of M tuberculosis and other mycobacterial species. Methods: The HT-SPOTi method was validated not only with known drugs but also with a library of 47 confirmed anti-TB active compounds published in the ChEMBL database. Three over-the-counter non-steroidal anti-inflammatory drugs were also included in the screening. The 2-arylpropanoic acids, including IBP, were comprehensively evaluated against phenotypically and physiologically different strains of mycobacteria, and their cytotoxicity was determined against murine RAW264.7 macrophages. Furthermore, a comparative bioinformatic analysis was employed to propose a potential mycobacterial target. Results: IBP showed antitubercular properties while carprofen was the most potent among the 2-arylpropanoic class. A 3,5-dinitro-IBP derivative was found to be more potent than IBP but equally selective. Other synthetic derivatives of IBP were less active, and the free carboxylic acid of IBP seems to be essential for its anti-TB activity. IBP, carprofen and the 3,5-dinitro-IBP derivative exhibited activity against multidrug-resistant isolates and stationary phase bacilli. On the basis of the human targets of the 2-arylpropanoic analgesics, the protein initiation factor infB (Rv2839c) of M tuberculosis was proposed as a potential molecular target. Conclusions: The HT-SPOTi method can be employed reliably and reproducibly to screen the antimicrobial potency of different compounds. IBP demonstrated specific antitubercular activity, while carprofen was the most selective agent among the 2-arylpropanoic class. Activity against stationary phase bacilli and multidrug-resistant isolates permits us to speculate a novel mechanism of antimycobacterial action. Further medicinal chemistry and target elucidation studies could potentially lead to new therapies against TB

Multi-residue analysis of pharmaceuticals in Belgian surface water : a novel screening-to-quantification approach using large-volume injection liquid chromatography coupled to high-resolution mass spectrometry

The ever growing number of emerging micropollutants such as pharmaceuticals requests rapid and sensitive full-spectrum analytical techniques. Time-of-flight highresolution mass spectrometry (TOF-HRMS) is a promising alternative for the state-ofthe- art MS/MS instruments because of its ability to simultaneously screen towards a virtually unlimited list of suspect compounds and to perform target quantification. The challenge for such suspect screening is to develop a strategy which minimizes the false negative rate without restraining numerous false positives. At the same time, omitting laborious sample enrichment through large-volume injection ultraperformance liquid chromatography (LVI-UPLC) is advantageous avoiding selective preconcentration. A novel suspect screening strategy was developed using LVI-UPLC-TOF-MS aiming the detection of 69 multi-class pharmaceuticals in surface water without the a priori availability of analytical standards. As a novel approach, the screening takes into account the signal intensity-dependent accurate mass error, hereby assuring the detection of 95% of pharmaceuticals present in surface water. Subsequently, the validation and applicability of the full-spectrum method for target quantification of the 69 pharmaceuticals in surface water is discussed. Analysis of five Belgian river water samples revealed the occurrence of 17 pharmaceuticals in a concentration range of 17 ng L-1 up to 3.1 μg L-1

The Frozen Core Approximation and Nuclear Screening Effects in Single Electron Capture Collisions

Fully Differential Cross Sections (FDCS) for single electron capture from helium by heavy ion impact are calculated using a frozen core 3-Body model and an active electron 4-Body model within the first Born approximation. FDCS are presented for H+, He2+, Li3+, and C6+ projectiles with velocities of 100 keV/amu, 1 MeV/amu, and 10 MeV/amu. In general, the FDCS from the two models are found to differ by about one order of magnitude with the active electron 4-Body model showing better agreement with experiment. Comparison of the models reveals two possible sources of the magnitude difference: the inactive electron's change of state and the projectile-target Coulomb interaction used in the different models. Detailed analysis indicates that the uncaptured electron's change of state can safely be neglected in the frozen core approximation, but that care must be used in modeling the projectile-target interaction

Desorption electrospray ionization-high resolution mass spectrometry for the screening of veterinary drugs in cross contaminated feddstuffs

In this study, a desorption electrospray ionization-high resolution mass spectrometry (DESI-HRMS) screening method was developed for fast identification of veterinary drugs in cross-contaminated feedstuffs. The reliable detection was performed working at high resolution (70,000 full with half maximum, FWHM) using an orbitrap mass analyser. Among the optimized DESI parameters, the solvent (acetonitrile-water, 80:20, v/v) and the sample substrate (poly-tetrafluoroethylene, PTFE) were critical to obtain the best sensitivity. To analyse the solid feed samples, different approaches were tested and a simple solid-liquid extraction and the direct analysis of an aliquot (2 μL) of the extract after let it dry on the PTFE printed spot provided the best results. The identification of the veterinary drugs (target and non-target) in the cross-contaminated feedstuffs based on the accurate mass measurement and the isotopic pattern fit was performed automatically using a custom-made database. The positive crosscontaminated feed samples were quantified by ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The results obtained demonstrate that DESI-HRMS can be proposed as a fast and suitable screening method to identify positive cross-contaminated feedstuffs reducing the number of samples to be subsequently quantified by UHPLC-MS/MS thus improving the productivity in quality control laboratories