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Mass-MetaSite

High-Throughput MetID

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Mass-MetaSite is a new approach for the automatic identification of metabolites from Liquid Chromatography - Mass Spectrometry data, reducing manual analysis from several hours to only a few minutes per compound [1]. The program is able to assign chemical structures to each automatically detected chromatographic peak based on the MS and MS/MS fragmentation pattern of the substrates and metabolites. Validation has been performed using over 400 metabolite incubations in recombinant and/or Human Liver microsomes, yielding a top-ranked prediction success rate of >95%. The same accuracy has been reached in an in-vivo metabolite identification exercise [2].

From data acquisition to metabolite structure elucidation in 2 minutes.

Mass-MetaSite screenshots

A revolution in Met ID for Drug Discovery

  • Reading of the most common file formats.
  • Agilent Q-Tof(*.d): AutoMS and full scan at multiple energies of collision.
  • Waters (*.raw): MSe and MSMS (MassLynx needs to be installed).
  • Thermo-Fisher (*.RAW): Ion-Trap and Orbitrap Data Dependent Scan, Exactive, Q-Exactive.
  • ABSCiex *.wiff file format.
  • Bruker (*.d): QTof data dependent scan.

New features in MassMetaSite 3.2.0

  • Batch processor: Auto-processing of experiment files
  • Multiple process batches
  • Improved ping to WebMetabase upload handler
  • Process Waters Q-TOF Data Dependent raw files
  • Updated Agilent Mass Hunter Data Access Component library
  • Updated default GSH fragment and ions
  • Optional summing of adduct areas
  • Lower memory consumption when generating markush depiction
  • Fixed importing of charged structures having heavy atoms
  • Fixed mass and ppm of double charge metabolite in xlsx reports
  • Added reactions: "Difluoromethylation", nitro reduction and the beta hydroxyl acid oxidation
  • Reviewed "Iminium cyanide conjugation" patterns

Features (v3.2)

  • Exclusion List for m/z values made available for MS peaks.
  • Improved chromatogram peak correlation measurement for a more accurate filtering of the MS spectrum.
  • Customizable neutral loss and fragment ion definitions for GSH metabolites detection.
  • Added cyanide and methylhydroxylamine trapping.
  • Easy activation/deactivation of uncommon reactions.
  • Improved discarding of metabolites peaks coming from background noise.
  • Importing and exporting of GUI and batch processor settings.
  • Processing of Radio files now supported by the batch processor.
  • Automatic filtering of unusual metabolites for Markush simplification.
  • Typical Glucuronide neutral loss (-176) taken into account for MetId.
  • SD File format exporting.
  • Activation/Deactivation of double-charged peak search. Improved isotopic pattern checking for double-charged ions detection.
  • Better smoothing algorithm for chromatogram peak detection. Smoothing level can now be fine tuned inside the settings.
  • Batch processor sample list wizard for direct interaction with webmetabase.
  • UltraViolet handling.
  • Automatic report system.
  • Batch processor: SSL connection for file transfer
  • Several new instruments and acquisition modes are supported.
  • Adduct formation: GSH trapping peak finding algorithm.
  • Direct connection to design tools:
    • MetaDesign module available, download pre-computed database fragments here. Uncompress the downloaded files and select them when using the MetaDesign module.
    • 32D
  • Automatic peak detection.
  • Chromatogram zoom function.
  • Addition of metabolic reactions: i.e. ketone reduction, oxidative dehalogenation.
  • Filtering options:
    • Absolute signal.
    • Total number of metabolites.
    • Ignore unknowns.
  • MetaSite 4.2.0 Site of Metabolism prediction.
  • Minor isotope filtering bug fix.
  • Support neutral loss and fragment ion detection for double charge GSH adducts.
  • Improved noise perception during metabolite peak detection.
  • Automatically discard predictions according to its score value.
  • Automatically merge MS/MS spectra with different charge states for the parent ion.
  • Reviewed "Carbamate hydrolysis" patterns and products.
  • Added reactions: "N-Sulphenyl Oxidation", "Desulphoxidation" and "Alkoxy Ipso Substitution".
  • Support Bruker Q-TOF autoMSMS acquisitions.
  • Handling of multiple charge ions (mass list generation, peak detection, area computation, structural assignment).
  • Analysis of peptide data (special import, skip SOM computation, custom fragmentation).
  • Explicit filtering by isotope pattern.
  • Assignment of metabolite fragments structure by using metabolite spectrum only.
  • Reduce number of false positives during GSH detection.
  • Fix speed and crash issues when using 3 metabolite generations.
  • Proper handling of Xevo G2 spectrum peaks when generating chromatogram peaks.
  • Added reactions: "Aliphatic oxidative defluorination", "GSH Conjugation (dearylation)", hydrolysis of primary amides.
  • Batchprocessor setting/mode to process data for calibration curves.
  • New Batchprocessor tool to create WebMetabase Protocol Instances/Batches on sample list import time.

Please login to see an overview of the Mass-MetaSite capabilities.

References