Journal ArticleDOI
Applying 'Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra' (SWATH) for systematic toxicological analysis with liquid chromatography-high-resolution tandem mass spectrometry.
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TLDR
Deconvolution of generated ion maps was found to be essential for unravelling the full identification power of LC-MS/MS with SWATH, which is capable of identifying more compounds at lower concentration levels than DDA does.Abstract:
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become an indispensable analytical technique in clinical and forensic toxicology for detection and identification of potentially toxic or harmful compounds. Particularly, non-target LC-MS/MS assays enable extensive and universal screening requested in systematic toxicological analysis. An integral part of the identification process is the generation of information-rich product ion spectra which can be searched against libraries of reference mass spectra. Usually, ‘data-dependent acquisition’ (DDA) strategies are applied for automated data acquisition. In this study, the ‘data-independent acquisition’ (DIA) method ‘Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra’ (SWATH) was combined with LC-MS/MS on a quadrupole-quadrupole-time-of-flight (QqTOF) instrument for acquiring informative high-resolution tandem mass spectra. SWATH performs data-independent fragmentation of all precursor ions entering the mass spectrometer in 21m/z isolation windows. The whole m/z range of interest is covered by continuous stepping of the isolation window. This allows numerous repeat analyses of each window during the elution of a single chromatographic peak and results in a complete fragment ion map of the sample. Compounds and samples typically encountered in forensic casework were used to assess performance characteristics of LC-MS/MS with SWATH. Our experiments clearly revealed that SWATH is a sensitive and specific identification technique. SWATH is capable of identifying more compounds at lower concentration levels than DDA does. The dynamic range of SWATH was estimated to be three orders of magnitude. Furthermore, the >600,000 SWATH spectra matched led to only 408 incorrect calls (false positive rate = 0.06 %). Deconvolution of generated ion maps was found to be essential for unravelling the full identification power of LC-MS/MS with SWATH. With the available software, however, only semi-automated deconvolution was enabled, which rendered data interpretation a laborious and time-consuming process.read more
Citations
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Journal ArticleDOI
Identification of small molecules using accurate mass MS/MS search.
Tobias Kind,Hiroshi Tsugawa,Tomas Cajka,Yan Ma,Zijuan Lai,Sajjan S. Mehta,Gert Wohlgemuth,Dinesh Kumar Barupal,Megan R. Showalter,Masanori Arita,Oliver Fiehn,Oliver Fiehn +11 more
TL;DR: Parameters that influence search results, such as mass accuracy, precursor ion isolation width, intensity thresholds, centroiding algorithms, and acquisition speed are critically discussed.
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Computational Metabolomics: A Framework for the Million Metabolome.
Karan Uppal,Douglas I. Walker,Douglas I. Walker,Ken Liu,Shuzhao Li,Young-Mi Go,Dean P. Jones +6 more
TL;DR: The present review looks at progress in computational metabolomics to provide probability-based annotation linking ions to known chemicals and serve as a foundation for unambiguous designation of unidentified ions for toxicologic study.
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Orbitrap technology for comprehensive metabolite-based liquid chromatographic-high resolution-tandem mass spectrometric urine drug screening - exemplified for cardiovascular drugs.
TL;DR: The novel LC-HR-MS/MS method allowed fast, simple, and robust urine screening, particularly for cardiovascular drugs showing the usefulness of Orbitrap technology for drug testing.
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Trends in the application of high-resolution mass spectrometry for human biomonitoring: An analytical primer to studying the environmental chemical space of the human exposome.
TL;DR: This review covers recent trends and advances of HRMS in human biomonitoring studies, and data acquisition and mining, and the challenges and prospects for future research.
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Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry
TL;DR: Current capabilities, strategies, and challenges will be reviewed for sample preparation, mass spectrometry, chromatography, and data processing workflows, and considerations to increase the accuracy and speed of identifying unknown molecular species will be addressed.
References
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Journal ArticleDOI
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
Ludovic C Gillet,Pedro Navarro,Stephen Tate,Hannes L. Röst,Nathalie Selevsek,Lukas Reiter,Ron Bonner,Ruedi Aebersold,Ruedi Aebersold +8 more
TL;DR: A new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest is presented, using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method.
Journal ArticleDOI
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
TL;DR: The proposed method is based on the sequential isolation and fragmentation of precursor windows within the ion trap until a desired mass range has been covered, and showed improvements in signal-to-noise ratio over corresponding chromatograms generated from mass spectrometry scans.
Journal ArticleDOI
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
Hannes L. Röst,George Rosenberger,Pedro Navarro,Ludovic C Gillet,Saša M. Miladinović,Olga T. Schubert,Witold Wolski,Ben C. Collins,Johan Malmström,Lars Malmström,Ruedi Aebersold +10 more
TL;DR: This research presents a novel and scalable approaches that allow for real-time measurement of the response of the immune system to treatments such as chemotherapy and immunotherapy.
Journal ArticleDOI
Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures
Guo-Zhong Li,Johannes P. C. Vissers,Jeffrey C. Silva,Jeffrey C. Silva,Dan Golick,Marc V. Gorenstein,Scott J. Geromanos +6 more
TL;DR: A novel database search algorithm is presented for the qualitative identification of proteins over a wide dynamic range, both in simple and complex biological samples, providing approximately 20% more protein identifications, compared to a more conventional data directed approach using the same identification criteria.
Journal ArticleDOI
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system
Ben C. Collins,Ludovic C Gillet,George Rosenberger,George Rosenberger,Hannes L. Röst,Hannes L. Röst,Anton Vichalkovski,Matthias Gstaiger,Ruedi Aebersold,Ruedi Aebersold +9 more
TL;DR: The consistent and reproducible quantification of 1,967 proteins across all stimulation time points provided insights into the 14-3-3β interactome and its dynamic changes following IGF1 stimulation, establishing AP-SWATH as a tool to quantify dynamic changes in protein-complex interaction networks.
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