WebMetabase is an application to archive, process, report and explore Metabolite Identification (Met ID) data from different experimental sources. Technically, it is a Java application that runs on a Java application server that connects to a database server, which is accessible to the user by a web browser. Therefore, WebMetabase is running on a internal server that should be reachable by anyone in the organization through the Intranet.
Since the application has been developed as independent of the database server, it can run in multiple systems (MySQL, Oracle, Microsoft SQL, etc..). Once the Java application and database servers are set up the deployment of the application is simple, reducing the maintenance time.
WebMetabase uses as input the files generated by MassMetaSite/Metabolite Pilot/Manually generated XML that can be automatically or manually upload to the server. The instruments are connected to a computer, where the raw data files are processed by Mass-MetaSite and the result files are sent to the WebMetabase server. Once the file is received by WebMetabase they are located in a section of the database call “Pending Experiments” waiting for the review and approval of the Met ID experts.
After the save and approval of the expert the state of the experiments is moved from “Pending” to “approved” and they are then visible to the rest of the organization.
WMB Training Documents:
- Tutorial_WMB_01. WebMetabase general definitions: Protocol definition
- Tutorial_WMB_02. MMS-WMB connection: The sample list and MMS batch process
- Tutorial_WMB_03. MMS-WMB connection: The sample list and MMS batch process II
- Tutorial_WMB_04. Automation Workflow: Starting an experiment from an instrument sample list
- Tutorial_WMB_05. GSH Experiment using the Autoprocess of the Batch Processor
- Tutorial_WMB_06 Approval process
- Tutorial_WMB_07. Analysis tools: Single Experiment
- Tutorial_WMB_08. Multi Experiment Analysis Tools: SMRt: Structure Metabolism Relationship table
- Tutorial_WMB_09. Multi Experiment Analysis Tools: Cluster View & Comparator
Pharma – Data Analysis – Met ID
Articles:
- Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Applications
- October 2020. Goracci L, Desantis J, Valeri A, Castellani B, Eleuteri M, Cruciani G.J
- Metabolite Identification Using An Ion Mobility-Enhanced Data-Independent Acquisition Strategy and Automated Data Processing. Rapid Commun Mass Spectrom
- June 2020. Radchenko T; Kochansky CJ; Cancilla M; Wrona MD; Mortishire-Smith RJ; Kirk J; Murray G; Fontaine F; Zamora I
- Development, optimization and implementation of a centralized metabolic soft spot assay
- April 2017. Paiva AA; Klakouski C; Li S; Johnson BM; Shu YZ; Josephs J; Zvyaga T; Zamora I; Shou WZ
- Metabolism study and biological evaluation of bosentan derivatives
- October 2016. Lepri S, Goracci L, Valeri A, Cruciani G.
- Software-aided structural elucidation in drug discovery
- November 2015. Ahlqvist M; Leandersson C; Hayes MA; Zamora I; Thompson RA
- High-throughput, computer assisted, specific MetID. A revolution for drug discovery
- Spring 2013. Zamora I; Fontaine F; Serra B; Plasencia G
- Software automation tools for increased throughput metabolic soft-spot identification in early drug discovery
- May 2013. Zelesky V; Schneider R; Janiszewski J; Zamora I; Ferguson J; Troutman M
- Update on hydrocodone metabolites in rats and dogs aided with a semi-automatic software for metabolite identification MassMetaSite
- May 2013. Li AC; Chovan JP; Yu E; Zamora I
- Enhanced metabolite identification with MS(E) and a semi-automated software for structural elucidation
- November 2010. Bonn B; Leandersson C; Fontaine F; Zamora I
Posters:
- Kinetic analysis during the metabolite identification process
- 05 June 2016. 64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX (United States of America)
- Development of higher-thoughput metabolic soft spot assay with integrated assessment of Glutathione adduct formation
- 05 June 2016. 64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX (United States of America)
Videos:
- PROTAC Metabolite Identification
- Practical Applications for Drug Discovery 2020 Webinar. Ismael Zamora
- Automation of Metabolite Identification
- Practical Applications for Drug Discovery 2020 Webinar. Ismael Zamora
- Spatial Localization and identification of Drug and Metabolites
- Practical Applications for Drug Discovery 2020 Webinar. Sara Tortorella, Giulia Coliva
Pharma – Data Analysis – Reactive Metabolite Screening
Articles:
- Post-acquisition analysis of untargeted accurate mass quadrupole time-of-flight MS(E) data for multiple collision-induced neutral losses and fragment ions of glutathione conjugates
- December 2014. Brink A; Fontaine F; Marschmann M; Steinhuber B; Cece EN; Zamora I; Pähler A
- Enhancing throughput of glutathione adduct formation studies and structural identification using a software-assisted workflow based on High Resolution Mass Spectrometry (HRMS) data
- October 2016. E.N. Cece-Esencan, F. Fontaine, G. Plasencia, M. Teppner, A. Brink, A. Pahler, I. Zamora.
- Software-aided cytochrome P450 reaction phenotyping and kinetic analysis in early drug discovery
- January 2016. Cece-Esencan EN; Fontaine F; Plasencia G; Teppner M; Brink A; Pähler A; Zamora I
Biopharma – Data Analysis – Peptide Metabolite Identification
Articles:
- WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source
- February 2019. Radchenko T; Fontaine F; Morettoni L; Zamora I
- Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry
- November 2017. Radchenko T; Brink A; Siegrist Y; Kochansky C; Bateman A; Fontaine F; Morettoni L; Zamora I
Posters:
- Software assisted analysis for Peptide Catabolism
- Institute for Research in Biomedicine (IRB Barcelona) 35 EPS European Peptide Symposium, Dublin (Ireland) … August 2018
- Peptide catabolite identification using HDMSE Data and MassMetaSite processing
- 66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego (United States of America) … 06 June 2018
- Peptide metabolism: High resolution mass Spectrometry tool to investigate peptide structure and amine bond metabolic susceptibility
- American Peptide Symposium, Whistler (Canada)… 17 June 2017
- Peptide metabolism: Identification of Metabolite structures of GLP-1 receptor agonists in different in-vitro systems using high resolution mass spectrometry
- 64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX (United States of America) … 05 June 2016
Videos:
- Metabolite ID For Peptides Made Simple
- Practical Applications for Drug Discovery 2020 Webinar. Tatiana Radchenko
- Proprietary Peptide Visualization Within MassMetaSite
- Practical Applications for Drug Discovery 2020 Webinar. Tatiana Radchenko
Biopharma – Data Analysis – Peptide Degradation
Posters:
- Automatization of structural elucidation workflow for detecting degradation impurities in Peptides
- February 2020. Elisabeth Ortega-Carrasco, Blanca Serra, Ismael Zamora
- High resolution Mass Spectroçmetry with automated data analysis to support structural elucidation of degradation impurities of small peptides
- AAPS 2019 PHARMSCI 360, San Antonio (United States of America)… 03 November, 2019
Videos:
- Proprietary Peptide Visualization Within MassMetaSite
- Practical Applications for Drug Discovery 2020 Webinar. Tatiana Radchenko
Biopharma – Data Analysis – Synthesis
Posters:
- Automatization of structural elucidation workflow for detecting degradation impurities in Peptides
- February 2020. Elisabeth Ortega-Carrasco, Blanca Serra, Ismael Zamora
- High resolution Mass Spectrometry with automated data analysis to support structural elucidation of degradation impurities of small peptides
- AAPS 2019 PHARMSCI 360, San Antonio (United States of America)… 03 November, 2019
Biopharma – Prediction – Catalysis Prediction
Articles:
- Software-aided workflow for predicting protease-specific cleavage sites using physicochemical properties of the natural and unnatural amino acids in peptide-based drug discovery
- January 2019. Radchenko T; Fontaine F; Morettoni L; Zamora I
