Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS

Schymanski, Emma L.; Gerlich, Michael; Ruttkies, Christoph; Neumann, Steffen

doi:10.5702/massspectrometry.s0036

Cited by 17 publications

(17 citation statements)

References 18 publications

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“…In terms of non-target identification, while some participants determine the molecular formula first, followed by elucidation on the basis of the one (or several possible) molecular formulas, other participants went straight to identification with an exact mass. The latter strategy, although resulting in more candidates, has been shown recently to be more effective from a data processing point of view [72] (it is for example easier to select candidates with one or some formula(s) from an exact mass search than to merge the results of several separate calculations).…”

Section: Data Processing Aspects Hr-ms/msmentioning

confidence: 99%

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

et al. 2015

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In this article, a dataset from a collaborative non-target screening trial organized 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 spectrometric 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 highlight major challenges such as 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. While 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 non-target analytical techniques are already considerably harmonized between the participants, but the data processing remains time-consuming. Although the dream of a "fully-automated identification workflow" remains elusive in the short-term, important steps in this direction have been taken, exemplified in 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.

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Section: Data Processing Aspects Hr-ms/msmentioning

confidence: 99%

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

et al. 2015

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“…Molecular formulas and tandem mass spectra are then searched in natural product databases and/or spectral libraries. In recent years, various computational tools have been developed to assist in the process (Allen et al, 2015; Duhrkop et al, 2015; Ridder et al, 2014; Scheubert et al, 2013; Schymanski et al, 2014a; Yang et al, 2013). …”

Section: Introductionmentioning

confidence: 99%

CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry

Nikolić

2017

Phytochemistry Letters

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The Critical Assessment of Small Molecule Identification (CASMI) contest is an initiative designed as an unbiased test of manual and automated strategies for the identification of small molecules from raw mass spectrometric data. In this contest, the participants are provided a set of high resolution MS and MS/MS data and asked to identify the unknown structure. CASMI 2016 is the fourth round of this contest in which the author participated in Category 1: Best Identification of Natural Products using a manual approach. The provided high resolution mass spectrometric data were interpreted manually using a combination of fragment and neutral loss analysis, literature consultation, manual database searches, deductive logic and experience. Out of 18 challenges, the author submitted correct structures as lead candidates for 14 challenges and 2nd ranked candidate for four challenges and was declared the winner of this category Pitfalls and challenges encountered during data interpretation are discussed.

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“…EICs generated for 121.0648 from the scan segments with collision energies at 15 eV and 35 eV (Fig SI.5) show additional peaks from those previously identified that were not included in our suspect list. The additional peaks could be significant and can be further analyzed using non-target strategies described by Schymanski et al 2013 [36].…”

Section: Common Fragments' Methodsmentioning

confidence: 99%

A data-independent acquisition workflow for qualitative screening of new psychoactive substances in biological samples

et al. 2015

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Identification of new psychoactive substances (NPS) is challenging. Developing targeted methods for their analysis can be difficult and costly due to their impermanence on the drug scene. Accurate mass-mass spectrometry (AMMS) using a quadrupole time-of-flight (QTOF) analyzer can be useful for wide-scope screening since it provides sensitive, full-spectrum MS data.Our article presents a qualitative screening workflow based on data-independent acquisition mode (All-ions MS/MS) on liquid chromatography (LC) coupled to QTOFMS for the detection and identification of NPS in biological matrices. The workflow combines and structures fundamentals of target and suspect screening data processing techniques in a structured algorithm. This allows the detection and tentative identification of NPS and their metabolites.We have applied the workflow to two actual case studies involving drug intoxications where we detected and confirmed the parent compounds ketamine, 25B-NBOME, 25C-NBOMe and several predicted Phase I and II metabolites not previously reported in urine and serum samples. The screening workflow demonstrates the added value for the detection and identification of NPS in biological matrices.

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Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS

Cited by 17 publications

References 18 publications

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

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

CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry

A data-independent acquisition workflow for qualitative screening of new psychoactive substances in biological samples

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