Database supported candidate search for Metabolite identification

Hildebrandt, Christian; Wolf, Sebastian I.; Neumann, Steffen

doi:10.1515/jib-2011-157

Cited by 14 publications

(13 citation statements)

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“…If we increased the error margins further, we found two formulas with an error of approximately 100 ppm (C 7 H 5 O, exact mass 105.0335, -100.0 ppm and C 4 H 9 O 3 , exact mass 105.0546, 101.4 ppm), of which the first could be rationalised quite easily with the structure of o-anisic acid. Several potential substructures with this first formula exist in the MassStruct system from Hildebrandt et al [34] when performing a query for fragments between 105.0345 and 105.0545 (results provided by S. Neumann, IPB; see Acknowledgements). The formula we suspect, however, is C 6 H 5 N 2 , exact mass 105.0447, 6.9 ppm error, which can only be achieved by adding N 2 to the formula.…”

Section: Including Peaks With 2n and O During Subformula Assignmentmentioning

confidence: 99%

Automatic recalibration and processing of tandem mass spectra using formula annotation

Stravs¹,

Schymanski

Singer³

et al. 2012

J. Mass. Spectrom.

117

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High accuracy, high resolution tandem mass spectrometry (MS/MS) is becoming more common in analytical applications, yet databases of these spectra remain limited. Databases require good quality spectra with sufficient compound information, but processing, calibration, noise reduction and retrieval of compound information are time-consuming tasks that prevent many contributions. We present a comprehensive workflow for the automatic processing of MS/MS using formula annotation for recalibration and cleanup to generate high quality spectra of standard compounds for upload to MassBank (www.massbank.jp). Compound information is retrieved via Internet services. Reference standards of 70 pesticides were measured at various collision energies on an LTQ-Orbitrap XL to develop and evaluate the workflow. A total of 944 resulting spectra are now available on MassBank. Evidence of nitrogen adduct formation during MS/MS fragmentation processes was found, highlighting the benefits high accuracy MS/MS offers for spectral interpretation. A database of recalibrated, cleaned-up spectra resulted in the most correct spectra ranked in first place, regardless of whether the search spectra were recalibrated or not, whereas the average rank of the correct molecular formula was improved from 2.55 (uncalibrated) to 1.53 when using recalibrated MS/MS data. The workflow is available as an R package RMassBank capable of generating MassBank records from raw MS and MS/MS data and can be adjusted to process data acquired with different settings and instruments. This workflow is a vital step towards addressing the need for more high quality, high accuracy MS/MS spectra in spectral databases and provides important information for spectral interpretation.

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Section: Including Peaks With 2n and O During Subformula Assignmentmentioning

confidence: 99%

Automatic recalibration and processing of tandem mass spectra using formula annotation

Stravs¹,

Schymanski

Singer³

et al. 2012

J. Mass. Spectrom.

117

View full text Add to dashboard Cite

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“…Enriched data collection may be of help in predicting metabolic pathways and find probable metabolites [104,105], also lead to the improvement of SOM prediction accuracy; especially those models are dependent on descriptor or knowledge. For empirical models and knowledge-based expert system, a large amount of in vivo and in vitro experimental data are required to apply to data analysis tools and machine learning approaches.…”

Section: Some Helpful Databasesmentioning

confidence: 99%

In Silico Prediction of Cytochrome P450-Mediated Site of Metabolism (SOM)

Liu¹,

Shen²,

Li³

et al. 2013

Protein and Peptide Letters

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Drug metabolism is a major consideration for modifying drug clearance and also a primary source for drug metabolite-induced toxicity. Cytochromes P450 (CYPs) are the major enzymes involved in drug metabolism and bioactivation, accounting for almost 75% of the total drug metabolism. Predicting the sites of cytochrome P450-mediated metabolism of drug-like molecules using in silico methods would be highly beneficial and time efficient. An ideal system would enable researchers to make a confident elimination decision based purely on the structure of a new compound. In this review, several tools and models for predicting probable site of metabolism (SOM) have been compared and discussed. The methods are generally based on enzyme structure, ligand structure, and combined methods. Although all the methods have certain accuracy and considerable progress has been made, the results of the calculations still need careful inspection.

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“…In the NORMAN MassBank, mass spectral records from different instrument types, ionisation techniques and collision energies obtained from standards and environmental samples provided by NOR-MAN members are included. MassBank offers sophisticated, vendor-independent storage and search options for any kind of high and low resolution mass spectra including, for example, EI-MS, ToF-MS and FT-MS. MassBank was recently combined with the in silico fragmentation tool MetFrag [16] (http://msbi.ipb-halle.de/ MetFrag) to build up MetFusion (http://msbi.ipb-halle/ MetFusion) and linked as a database search option within MzMine (available from version 2.5). This approach helps to overcome problems with different instruments and/or experimental settings, and supports the identification of unknown and emerging compounds using conventional and modern mass spectrometers coupled to gas or liquid chromatography.…”

Section: Effect-directed Analysis For Identification Of Relevant Emermentioning

confidence: 99%

The NORMAN Network and its activities on emerging environmental substances with a focus on effect-directed analysis of complex environmental contamination

2012

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The need to look beyond the conventional target pollutants when assessing the hazards of chemicals to human health and to ecosystems is now generally recognised as a priority issue in all environmental policy areas at both the European level and national level in the various countries. It has also become clear that it is not possible for individual countries alone to develop the knowledge and methodologies needed for measuring and evaluating the effects and associated risks of a vast number of emerging pollutants. Further to these priority needs, the NORMAN project (www.norman-network.net) was funded in 2005 by the European Commission in order to promote the creation of a permanent network among reference laboratories and research centres, in collaboration with the parties involved (industry, standardisation bodies, NGOs, etc.), to ensure (i) a more rapid and wide-scope exchange of data and information on the occurrence and effects of emerging substances, (ii) better data quality and comparability via validation and harmonisation of common measurement methods (chemical and biological) and monitoring tools, (iii) more transparent information (need for information, not just data) and (iv) the establishment of an independent and competent forum for the technical/scientific debate on issues related to emerging substances. NORMAN plays a significant role as an interface organisation between science and policy, with the advantage of speaking with a "bigger voice" to the European Commission and other public institutions. The activities of the network range from a scientific watch and the feeding of data on emerging substances into NORMAN databases (information gateway on emerging pollutants) to the organisation of working groups and workshops (producing position papers on research priorities), the setting-up of interlaboratory studies and the organisation of measurement campaigns. This article presents the objectives and scope of the activities of the NORMAN network, together with a summary of its concrete achievements after six years of existence. Moreover, the article gives a special insight in the work done by the NORMAN Working Group on effect-directed analysis for the identification of hazardous pollutants.

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Database supported candidate search for Metabolite identification

Cited by 14 publications

References 0 publications

Automatic recalibration and processing of tandem mass spectra using formula annotation

Automatic recalibration and processing of tandem mass spectra using formula annotation

In Silico Prediction of Cytochrome P450-Mediated Site of Metabolism (SOM)

The NORMAN Network and its activities on emerging environmental substances with a focus on effect-directed analysis of complex environmental contamination

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