Oniro is a web container that encapsulates a number of Mass Analytica solutions for structure elucidation, in-silico predictions, spectral database, search and reporting that could be used in multiple fields.
The platform is distributed together with the WebMetabase, Compound Library, WebChembase and WebQuant applications and it is way to manage user, settings, import exported files and access to the applications itself.
This application can give access to multiple desktops of server-based applications depending on the apps that the user wants to plug into the system.
The different apps can be activated by adding the license line to the code or by setting the connection in the user settings.
This web application controls:
- The user access to the different applications as well as the accessibility to the different functionalities inside the applications
- Definition of the workgroups
- Application Settings
- Import experiments from other Oniro installations
The entire Oniro system and databases are designed to be able to interpret, analyze and save Mass Spectra data. Also, the system can be used to report and design new compounds in drug discovery and development considering data from multiple sources (vendors, acquisition, experiments, departments, etc..).
- WMB Training Documents
- WCB Training Documents
- CL Training Documents
- WQ Training Documents
Articles:
- Prediction of peptide cleavage sites using protein language models and graph neural networks
- October 30, 2025. Paula Cifuentes, Ramon Adàlia, Ismael Zamora
- Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase
- June 2021. Stefano Bonciarelli, Jenny Desantis*, Laura Goracci, Lydia Siragusa, Ismael Zamora, Elisabeth Ortega-Carrasco*
- 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
- 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 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
- 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
- Enabling Efficient Late‐Stage Functionalization of Drug‐Like Molecules with LC‐MS and Reaction‐Driven Data Processing
- European Journal of Organic Chemistry, 2017. Huifang Yao, Yong Liu, Sriram Tyagarajan, Eric Streckfuss, Mikhail Reibarkh, Kuanchang Chen, Ismael Zamora, Fabien Fontaine, Laura Goracci, Roy Helmy, Kevin P. Bateman, Shane W. Krska
- 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.
- 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
- Software-aided structural elucidation in drug discovery
- November 2015. Ahlqvist M; Leandersson C; Hayes MA; Zamora I; Thompson RA
- 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
- 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:
- Software-aided approach designed to analyze and predict cleavage sites for peptides
- 73rd ASMS Conference on Mass Spectrometry. June 2025. Paula Cifuentes; Ramon Adalia; Ismael Zamora; Lisa O’Callaghan, Richard Gundersdorf
- Automation in Metabolite Identification Workflows with Software-Assisted Processing of Mass Spectrometry Data
- 73rd ASMS Conference on Mass Spectrometry. June 2025. Savannah M Mason; Ismael Zamora; Luca Morettoni; Paula Cifuentes; Ramon Adalia
- An automated software-assisted approach for exploring metabolic susceptibility and degradation products in macromolecules using High-Resolution Mass Spectrometry
- 72nd ASMS Conference on Mass Spectrometry. June 2024. Paula Cifuentes; Ismael Zamora; Fabien Fontaine; Albert Garriga; Luca Morettoni; Tatiana Radchenko
- Machine Learning-Assisted False Positive Detection in Metabolite Identification Workflows
- 72nd ASMS Conference on Mass Spectrometry. June 2024. Ramon Adàlia; Fabien Fontaine; Luca Morettoni; Ismael Zamora
- Automation of Routine HRMS Analysis using MassChemSite and WebChembase using lansoprazole forced degradation as case study
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August 2021. 61st Annual Land o’ Lakes Pharmaceutical Analysis Conference. Elisabeth Ortega-Carrasco, Luca Morettoni, Fabien Fontaine, Ismael Zamora
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- Automation of data analysis in High-Troughput Experimentation using WebChembase server application
- ESOC 2021. European Symposium on Organic Chemistry. Virtual Mini Symposium. July 2021
- A Case Study Of The MassChemSite Reaction Tracking Workflow: Detecting And Identifying Byproducts During PROTAC Synthesis
- 68th ASMS Conference on Mass Spectrometry and Allied Topics Reboot. Online. June 2020
- 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
- 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
- Structural Elucidation Tools To Enhance Organic Synthesis Productivity
- 66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego (United States of America). 06 June 2018
- Towards an automatic structure elucidation process in various chemical workflows by LC-HRMS and NMR data analysis
- 254th ACS National Meeting, Washington DC (United States of America) 20 August 2017
- An innovative algorithm to elucidate the structure of unknown compounds using tandem Mass Spectrometry and NMR data
- 65th ASMS Conference on Mass Spectrometry and Allied Topics, Indianapolis, IN (United States of America) 04 June 2017
- 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
- 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:
- Scalable Peptide MRM Transition Prediction for High-Throughput Proteomics via Hashing-Based Sequence Encoding
- 73rd ASMS Conference on Mass Spectrometry. June 2025
- Oniro: automation and standardization for workflow definition
- Customizable spectra signal colors
- WebMetabase & WebChembase: Fragment analysis validation for manual edited compound
- Compound Library: automation of Compound set definition
- 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
- PROTAC Metabolite Identification
- Practical Applications for Drug Discovery 2020 Webinar. Ismael Zamora
- DMPK Workflows: HT MS For Clearance Determination
- Practical Applications for Drug Discovery 2020 Webinar. Ismael Zamora
- Forced Degradation Studies For Chemicals
- Practical Applications for Drug Discovery 2020 Webinar. Elisabeth Ortega-Carrasco
- 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
- PROTAC Analysis: Analysis Of Chemical Reactions
- Practical Applications for Drug Discovery 2020 Webinar. Elisabeth Ortega-Carrasco
- Late Stage Functionalization Automation Of MS Driven Structure Elucidation
- Practical Applications for Drug Discovery 2020 Webinar. Elisabeth Ortega-Carrasco
