Computational mass spectrometry for small molecules

Scheubert, Kerstin; Hufsky, Franziska; Böcker, Sebastian

doi:10.1186/1758-2946-5-12

Cited by 134 publications

(119 citation statements)

References 242 publications

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“…The reasons for this are varied, including the lack of reproducibility between SI instruments and various settings and the relative newness of the technique, and are discussed in greater detail elsewhere (e.g. [13][14][15]). As a consequence, the identification of "unknown" environmental substances of interest measured with GC-EI-MS can often be performed with a spectral library, while substances measured with alternative ionization techniques generally require the parallel approaches of target, suspect and non-target screening.…”

Section: Introductionmentioning

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: Introductionmentioning

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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“…For example, the number of predicted compounds from a database search can be reduced by excluding compounds with predicted MS/MS spectra that do not match the observed [94]. Advancements in predictive fragmentation are being developed [95][96][97][98][99][100][101] and have been reviewed previously [76]. Examples of MS/MS fragmentation prediction tools include, but are not limited to, ACD/MS Fragmenter [102], MolFind [94], MetFrag [101], MIDAS (Metabolite Identification via Database Searching) [103] and SmartMass [91].…”

Section: Tandem Mass Spectrometrymentioning

confidence: 98%

“…Technical aspects of computational approaches to identification of small molecules has been reviewed previously [76]. The majority of MS data analysis software provided by instrument vendors includes functionality to generate a molecular formula for a particular m/z value and its theoretical isotopic pattern, which can be used as a reference.…”

Section: Identificationmentioning

confidence: 99%

Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry

Knolhoff

Croley

2016

Journal of Chromatography A

104

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“…The term "structure elucidation" usually refers to full de novo structure identification of a compound, including stereochemical assignments [5]. Thus, a combination of chromatographic techniques with multidimensional, namely tandem MS offers an adequate solution for bioproduct screening and compound identification.…”

Section: Introductionmentioning

confidence: 99%

Identification of lipophilic bioproduct portfolio from bioreactor samples of extreme halophilic archaea with HPLC-MS/MS

et al. 2014

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Extreme halophilic Archaea are a yet unexploited source of natural carotenoids. At elevated salinities, however, material corrosivity issues occur and the performance of analytical methods is strongly affected. 2The goal of this study was to develop a method for identification and downstream processing of potentially valuable bioproducts produced by Archaea. To circumvent extreme salinities during analysis, a direct sample preparation method was established to selectively extract both the polar and the non-polar lipid contents of extreme halophiles with hexane, acetone and the mixture of MeOH/MTBE/water, respectively.Halogenated solvents, as used in conventional extraction methods, were omitted due to environmental considerations and potential process scale-up. This study demonstrates the importance of sample preparation and the applicability of HPLC-MS/MS methods on real samples from extreme halophilic strains. Furthermore, from a biotechnological point-of-view, this study would like to reveal the relevance of using controlled and defined bioreactor cultivations instead of shake flask cultures in the early stage of potential bioproduct profiling.

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Computational mass spectrometry for small molecules

Cited by 134 publications

References 242 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

Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry

Identification of lipophilic bioproduct portfolio from bioreactor samples of extreme halophilic archaea with HPLC-MS/MS

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