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Nat Biotechnol ; 39(7): 846-854, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33767396


Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.

Proteômica/métodos , Espectrometria de Massas em Tandem , Arabidopsis/metabolismo , Biomarcadores/metabolismo , COVID-19/sangue , COVID-19/diagnóstico , Linhagem Celular , Humanos , Peptídeos/análise , Proteoma/análise , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Índice de Gravidade de Doença
Sci Total Environ ; 757: 144006, 2021 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-33310574


The coronavirus disease 2019 (COVID-19) has developed into a serious pandemic with millions of cases diagnosed worldwide. To fight COVID-19 pandemic, over 100 countries instituted either a full or partial lockdown, affecting billions of people. In Tyrol, first lockdown measures were taken on 10 March 2020. On 16 March 2020, a curfew went into force which ended on 1 May 2020. On 19 March 2020, Tyrol as a whole was placed in quarantine which ended on 7 April 2020. The governmental actions helped reducing the spread of COVID-19 at the cost of significant effects on social life and behaviour. Accordingly, to provide a comprehensive picture of the population health status not only input from medical and biological sciences is required, but also from other sciences able to provide lifestyle information such as drug use. Herein, wastewater-based epidemiology was used for studying temporal trends of licit and illicit drug consumption during lockdown and quarantine in the area of the Tyrolean capital Innsbruck (174,000 inhabitants). On 35 days between 12 March 2020 and 15 April 2020, loads of 23 markers were monitored in wastewater. Loads determined on 292 days between March 2016 and January 2020 served as reference. During lockdown, changes in the consumption patterns of recreational drugs (i.e. cocaine, amphetamine, 3,4-methylenedioxymethamphetamine, methamphetamine, and alcohol) and pharmaceuticals for short-term application (i.e. acetaminophen, codeine, and trimethoprim) were detected. For illicit drugs and alcohol, it is very likely that observed changes were linked to the shutdown of the hospitality industry and event cancelation which led to a reduced demand of these compounds particularly on weekends. For the pharmaceuticals, further work will be necessary to clarify if the observed declines are indicators of improved population health or of some kind of restraining effect that reduced the number of consultations of medical doctors and pharmacies.

COVID-19 , Águas Residuárias , Controle de Doenças Transmissíveis , Humanos , Pandemias , SARS-CoV-2 , Águas Residuárias/análise
Anal Methods ; 12(35): 4377-4386, 2020 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-32852487


This study reports the synthesis of the room temperature ionic liquid 1-propyloxy-3-ethoxyimidazolium bis(trifluoromethane)sulfonamide for the extraction of bergapten and bergamottin from hydroalcoholic cosmetic samples by means of dispersive liquid-liquid microextraction. Molecular structures of the final ionic liquid as well as intermediate products were confirmed by nuclear magnetic resonance spectroscopy. Analyses were performed with high performance liquid chromatography with subsequent diode array and fluorescence detection. The extraction procedure was optimized with the design of the experiment using a three level Box-Behnken approach. Applying the synthesized room temperature ionic liquid as extraction medium, the optimized workflow demonstrated high recoveries illustrating powerful isolation properties for furanocoumarins, which are comparable or even better than using typical extraction solvents. Moreover, the workflow was validated regarding instrumental limits, linearity, accuracy, repeatability and stability of analytes according to international guidelines. To test its applicability on a more complex matrix, hydroalcoholic cosmetic samples were analyzed. Despite highly complex matrices, accurate and precise quantification in the range of 0.04-1.25 µg mL-1 was achieved in spiked and unspiked samples, with bias <10% and RSD < 12%.

Cell Syst ; 11(1): 11-24.e4, 2020 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-32619549


The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.

Proteínas Sanguíneas/metabolismo , Infecções por Coronavirus/sangue , Pneumonia Viral/sangue , Proteômica/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , Betacoronavirus/isolamento & purificação , Biomarcadores/sangue , Proteínas Sanguíneas/análise , COVID-19 , Infecções por Coronavirus/classificação , Infecções por Coronavirus/patologia , Infecções por Coronavirus/virologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Pandemias/classificação , Pneumonia Viral/classificação , Pneumonia Viral/patologia , Pneumonia Viral/virologia , SARS-CoV-2 , Adulto Jovem
Anal Chim Acta ; 1101: 211-221, 2020 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-32029113


Furanocoumarins are a class of naturally occurring phototoxic substances widely spread throughout the Umbelliferae and Rutacea families of plants. Plant extract of these families (e.g. citrus extracts) are commonly used as ingredients in fragrances and cosmetic products. Due to their phototoxicity these substances are regulated within the European Union according to the European Regulation (EC) No. 1223/2009 on cosmetic products. The proposed analytical workflow aims to swiftly screen out and determine the amount of phototoxic furanocoumarins in natural cosmetics employing solid-phase extraction (SPE). Cosmetic samples were first extracted in methanol and subsequently diluted in 35% (v/v) methanol before being applied to solid-phase extraction. The extraction procedure allows extraction of the eight target compounds including the six marker-substances proposed by the International Fragrance Association (IFRA) from complex cosmetic samples with satisfactory recovery levels ranging from 84 to 116% with the exception of bergamottin (68-89%). HPLC-UV and ESI-MS were used for the analysis of the target compounds. Furanocoumarin quantification was performed by standard addition. The workflow was successfully validated according to the ISO 12787 international standard ("Cosmetics - Analytical methods- Validation criteria for analytical results using chromatographic techniques"). Results of the validation on standard solutions highlight a LOQ of 0.01 mg kg-1, acceptable linearity up to 1 mg/kg as well as good accuracy (Bias <15%) and precision (RSD <15%). Total furanocoumarin levels of the examined natural cosmetic products were in general in agreement with the European Regulation. However, it was shown that total levels of furanocoumarins might be significantly higher than assumed using the six proposed marker substances only.

Cromatografia Líquida/métodos , Cosméticos/análise , Furocumarinas/análise , Espectrometria de Massas/métodos , Extração em Fase Sólida/métodos , Luz , Limite de Detecção
Metabolites ; 9(1)2018 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-30583579


Tandem mass spectral databases are indispensable for fast and reliable compound identification in nontargeted analysis with liquid chromatography⁻high resolution tandem mass spectrometry (LC-HRMS/MS), which is applied to a wide range of scientific fields. While many articles now review and compare spectral libraries, in this manuscript we investigate two high-quality and specialized collections from our respective institutes, recorded on different instruments (quadrupole time-of-flight or QqTOF vs. Orbitrap). The optimal range of collision energies for spectral comparison was evaluated using 233 overlapping compounds between the two libraries, revealing that spectra in the range of CE 20⁻50 eV on the QqTOF and 30⁻60 nominal collision energy units on the Orbitrap provided optimal matching results for these libraries. Applications to complex samples from the respective institutes revealed that the libraries, combined with a simple data mining approach to retrieve all spectra with precursor and fragment information, could confirm many validated target identifications and yield several new Level 2a (spectral match) identifications. While the results presented are not surprising in many ways, this article adds new results to the debate on the comparability of Orbitrap and QqTOF data and the application of spectral libraries to yield rapid and high-confidence tentative identifications in complex human and environmental samples.