Resource Library

PRESENTATION

Oligonucleotides: degradation studies

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora1; Fabien Fontaine1; Tatiana Radchenko1; Bridget Becker2; Robert Greene2

POSTER

Automated identification of potential pesticides residues in fruit samples using HRMS data

70th ASMS Conference on Mass Spectrometry. June 2022

Elisabeth Ortega1; Ismael Zamora1; Pol Giménez1; Luca Morettoni1; Roberto Romero-Gonzalez2; Rosalía López-Ruiz2; Antonia Garrido Frenich2

POSTER

AI (ARTIFICIAL INTELLIGENCE) applied to enhance the DMPK experimental efficacy

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora; Ramon Adàlia; Tatiana Radchenko

POSTER

Automatic Quantification workflow using High Resolution Mass Spectrometry

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora1; Fabien Fontaine1; Pol Giménez1; Kevin P Bateman2; Christopher Konchansky2

POSTER

Improving metabolite identification for complex peptides using MassMetaSite

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora; Tatiana Radchenko; Fabien Fontaine; Albert Garriga

POSTER

Comparison of CID and EAD fragmentation with automated assignment for small molecule structure elucidation

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora1; Christopher Kochansky2; Fabien Fontaine1; Kevin P Bateman2; Jason Causon3; Jose Castro-Perez4; Rolf Kern5

POSTER

Automation of data analysis in High-Troughput Experimentation using WebChembase server application

ESOC 2021. European Symposium on Organic Chemistry. Virtual Mini Symposium. July 2021

Elisabeth Ortega-Carrasco,(1) Jenny Desantis,(2) Stefano Bonciarelli,(3) Laura Goracci,(3) Ismael Zamora(1)

POSTER

Automation of Routine HRMS Analysis for stress testing: lansoprazole as case study

61st Annual Land o’ Lakes Pharmaceutical Analysis Conference. August 2021

Elisabeth Ortega-Carrasco,(1) Jenny Desantis,(2) Stefano Bonciarelli,(3) Laura Goracci,(3) Ismael Zamora(1)

ARTICLE

Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase

J. Chem. Inf. Model. 2021, 61, 6, 2706–2719

Stefano Bonciarelli, Jenny Desantis*, Laura Goracci, Lydia Siragusa, Ismael Zamora, Elisabeth Ortega-Carrasco*

ARTICLE

Mass spectrometry imaging of phosphatidylcholine metabolism in lungs administered with therapeutic surfactants and isotopic tracers

Journal Of Lipid Research, 2021

Shane R. Ellis, Emily Hall, Madhuriben Panchal, Bryn Flinders, Jens Madsen, Grielof KosterRon.M.AHeeren, Howard W. Clark, Anthony D. Postle 

ARTICLE

Degradation studies of dimethachlor in soils and water by UHPLC-HRMS: putative elucidation of unknown metabolites

Pest Manag Sci 76(2):721-729. 2020.

López-Ruiz R; Romero-González R; Ortega-Carrasco E; Martínez Vidal JL; Garrido Frenich A

ARTICLE

Lipostar MSI: Comprehensive, Vendor-Neutral Software for Visualization, Data Analysis, and Automated Molecular Identification in Mass Spectrometry Imaging

J Am Soc Mass Spectrom. 2020 Jan 2;31(1):155-163. doi: 10.1021/jasms.9b00034. Epub 2019 Nov 21. PMID: 32881505.  

Tortorella S, Tiberi P, Bowman AP, Claes BSR, Ščupáková K, Heeren RMA, Ellis SR, Cruciani G. 

ARTICLE

Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Applications

Goracci L, Desantis J, Valeri A, Castellani B, Eleuteri M, Cruciani G.J Med Chem. 2020 Oct 22;63(20):11615-11638. doi: 10.1021/acs.jmedchem.0c00793. Epub 2020 Oct 7.PMID: 33026811  

Introduction

Our vision for Mass Spec Software development

Practical Applications for Drug Discovery 2020 Webinar introduction video

Ismael Zamora Rico

Solutions for Computational Chemist

Chemically-Aware Molecular And Atomic Descriptors For Medicinal Chemistry Applications

Practical Applications for Drug Discovery 2020 Webinar video

Sara Tortorella, Giovanni Bocci

Solutions for Chemistry

Late Stage Functionalization Automation Of MS Driven Structure Elucidation

Practical Applications for Drug Discovery 2020 Webinar video

Elisabeth Ortega-Carrasco

Solutions for Chemistry

Forced Degradation Studies For Chemicals

Practical Applications for Drug Discovery 2020 Webinar video

Solutions for Chemistry

PROTAC Analysis: Analysis Of Chemical Reactions

Practical Applications for Drug Discovery 2020 Webinar video

Elisabeth Ortega-Carrasco

Solutions for Chemistry

UNIFI Connection For Any Workflow

Practical Applications for Drug Discovery 2020 Webinar video

Elisabeth Ortega-Carrasco, Russell Mortishire-Smith, Christopher Henry

Solutions for Pharma DMPK

DMPK Workflows: HT MS For Clearance Determination

Practical Applications for Drug Discovery 2020 Webinar video

Ismael Zamora

Solutions for Pharma DMPK

PROTAC Metabolite Identification

Practical Applications for Drug Discovery 2020 Webinar video

Ismael Zamora

Solutions for Pharma DMPK

Automation of Metabolite Identification

Practical Applications for Drug Discovery 2020 Webinar video

Ismael Zamora

Solutions for Pharma DMPK

Data and prediction on the same place

Practical Applications for Drug Discovery 2020 Webinar video

Ismael Zamora

Spatial OMICS and MetID

Comprehensive, vendor-neutral, high-throughput imaging mass spectrometry data analysis

Practical Applications for Drug Discovery 2020 Webinar video

Sara Tortorella

Spatial OMICS and MetID

Ion Mobility MSI: Adding A New Dimension To Spatial Metabolomics

Practical Applications for Drug Discovery 2020 Webinar video

Sara Tortorella, Jens Soltwisch

Spatial OMICS and MetID

Spatial Localization And Identification Of Drug And Metabolites

Practical Applications for Drug Discovery 2020 Webinar video

Sara Tortorella, Giulia Coliva

Biopharma Solutions

Proprietary Peptide Visualization Within MassMetaSite

Practical Applications for Drug Discovery 2020 Webinar video

Tatiana Radchenko

Biopharma Solutions

Metabolite ID For Peptides Made Simple

Practical Applications for Drug Discovery 2020 Webinar video

Tatiana Radchenko

Solutions for OMICS

Untargeted And Targeted Lipidomics: From Raw Data To Bio-Pathways

Practical Applications for Drug Discovery 2020 Webinar video

Laura Goracci

Solutions for OMICS

Solutions For Flux Analysis in Lipidomics

Practical Applications for Drug Discovery 2020 Webinar video

Laura Goracci

Solutions for OMICS

Biomarkers Discovery And Beyond: The Trend Analysis

Practical Applications for Drug Discovery 2020 Webinar video

Alla Kloss, Laura Goracci

MassMetaSite 4.0

Introduction to MassMetaSite

Your tool for Metabolite Identification using Mass Spectrometry data: Small & Macro Molecules

WebMetabase - WebChembase

AutomaticMetID-reporting

POSTER

Automatization of structural elucidation workflow for detecting degradation impurities in Peptides

25 February, 2020 

Elisabeth Ortega-Carrasco1; Blanca Serra1; Ismael Zamora1 1 Lead Molecular Design S.L., Sant Cugat del Valles, Spain;

ARTICLE

LipostarMSI: Comprehensive, Vendor-Neutral Software for Visualization, Data Analysis, and Automated Molecular Identification in Mass Spectrometry Imaging

J Am Soc Mass Spectrom. 2020 Jan 2;31(1):155-163. doi: 10.1021/jasms.9b00034. Epub 2019 Nov 21. PMID: 32881505 

Tortorella S, Tiberi P, Bowman AP, Claes BSR, Ščupáková K, Heeren RMA, Ellis SR, Cruciani G.

ARTICLE

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.

POSTER

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

Laura Goracci1; Elisabeth Ortega-Carrasco2; Ismael Zamora2,3; Fabien Fontaine2; Jenny Desantis1

ARTICLE

Enrichment procedure based on graphitized carbon black and liquid chromatography-high resolution mass spectrometry for elucidating sulfolipids composition of microalgae

December 2019.

Antonelli M, Benedetti B, Cavaliere C, Cerrato A, La Barbera G, Montone CM, Piovesana S, Laganà A. Talanta

ARTICLE

Nutritional and lipidomics biomarkers of docosahexaenoic acid-based multivitamin therapy in pediatricRole of mitochondria and cardiolipins in growth inhibition of breast cancer cells by retinoic acid

Sci Rep. 2019 Feb 14;9(1):2045. doi: 10.1038/s41598-018-37209-y.PMID: 30765737; PMCID: PMC6375912.

Torquato P, Giusepponi D, Alisi A, Galarini R, Bartolini D, Piroddi M, Goracci L, Di Veroli A, Cruciani G, Crudele A, Nobili V, Galli F. 

ARTICLE

Role of mitochondria and cardiolipins in growth inhibition of breast cancer cells by retinoic acid

J Exp Clin Cancer Res. 2019 Oct 29;38(1):436. doi: 10.1186/s13046-019-1438-y. Erratum in: J Exp Clin Cancer Res. 2019 Dec 18;38(1):496. PMID: 31665044; PMCID: PMC6821005.

Terao M, Goracci L, Celestini V, Kurosaki M, Bolis M, Di Veroli A, Vallerga, A, Fratelli M, Lupi M, Corbelli A, Fiordaliso F, Gianni M, Paroni G, Zanetti A, Cruciani G, Garattini E.

ARTICLE

Computational solutions in redox lipidomics – Current strategies and future perspectives

Free Radic Biol Med. 2019 Nov 20;144:110-123. doi: 10.1016/j.freeradbiomed.2019.04.027. Epub 2019 Apr 26. PMID: 31035005. 

Ni Z, Goracci L, Cruciani G, Fedorova M.

POSTER

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 

ARTICLE

WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source. 

Bioinformatics 35(4):650-655 

Radchenko T; Fontaine F; Morettoni L; Zamora I, 2019.

ARTICLE

Lipidomics-Based Approach to Evaluating the Risk of Clinical Hepatotoxicity Potential of Drugs in 3D Human Microtissues.

Chem Res Toxicoly 2020 Jan 21;33(1):258-270. doi: 10.1021/acs.chemrestox.9b00364. Epub 2019 Dec 24. PMID: 31820940. 

Goracci L, Valeri A, Sciabola S, Aleo MD, Moritz W, Lichtenberg J, Cruciani, G. A Novel

POSTER

Automatic MS Data Analysis to reveal the metabolic pathways of pesticides in fruits and soils

256th ACS National Meeting, Boston, MA (United States of America) 21 August, 2018 

ARTICLE

Delving into the Polar Lipidome by Optimized Chromatographic Separation, High-Resolution Mass Spectrometry, and Comprehensive Identification with Lipostar: Microalgae as Case Study

Anal Chem. 2018 Oct 16;90(20):12230-12238. doi: 10.1021/acs.analchem.8b03482. Epub 2018 Sep 24. PMID: 30204416. 

 La Barbera G, Antonelli M, Cavaliere C, Cruciani G, Goracci L, Montone CM, Piovesana S, Laganà A, Capriotti AL

POSTER

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 

ARTICLE

From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions

J Med Chem. 2018 Jan. 

Cruciani G, Milani N, Benedetti P, Lepri S, Cesarini L, Baroni M, Spyrakis F, Tortorella S, Mosconi E, Goracci L.

POSTER

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 

ARTICLE

Lipostar, a Comprehensive Platform-Neutral Cheminformatics Tool for Lipidomics

Anal Chem. 2017 Jun 6;89(11):6257-6264. doi:10.1021/acs.analchem.7b01259. Epub 2017 May 12. PMID: 28471643. 

Goracci L, Tortorella S, Tiberi P, Pellegrino RM, Di Veroli A, Valeri A, Cruciani G.

ARTICLE

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

POSTER

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 

POSTER

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

ARTICLE

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, 2017. 

POSTER

Software Assisted Analysis For Peptide Catabolism

Institute for Research in Biomedicine (IRB Barcelona) 35 EPS European Peptide Symposium, Dublin (Ireland) 

Anna Escolà (1,2), Antoni Riera (1,2), Aurora Valeri (3), Ismael Zamora (4,5), Tatiana Radchenko (4,5) 1. 

ARTICLE

Structure-metabolism relationships in human- AOX: Chemical insights from a large database of aza-aromatic and amide compounds

2017 Apr 18

Lepri S, Ceccarelli M, Milani N, Tortorella S, Cucco A, Valeri A, Goracci L, Brink A, Cruciani G.

ARTICLE

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, 2017.

ARTICLE

Metabolism study and biological evaluation of bosentan derivatives 

October 2016

Susan LepriLaura GoracciAurora ValeriGabriele Cruciani

ARTICLE

Use of lipidomics to investigate sebum dysfunction in juvenile acne

June 2016

Camera E, Ludovici M, Tortorella S, Sinagra JL, Capitanio B, Goracci L, Picardo M.

POSTER

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 

POSTER

Fitting Kinetic equations derived from metabolic pathways to LC/MS-MS integrated peak areas

64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX (United States of America) 05 June 2016 

POSTER

Development of higher-thoughput metabolic soft spot assay with integrated assessment of Glutathione adduct formation

64th ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX (United States of America) 05 June 2016 

ARTICLE

Software-aided cytochrome P450 reaction phenotyping and kinetic analysis in early drug discovery

December 2015.

Cece-Esencan EN; Fontaine F; Plasencia G; Teppner M; Brink A; Pähler A; Zamora I, 2016. 

ARTICLE

Software-aided structural elucidation in drug discovery

November 2015.

Ahlqvist M; Leandersson C; Hayes MA; Zamora I; Thompson RA

ARTICLE

Phospholipidosis effect of drugs by adsorption into lipid monolayers. Colloids Surf B Biointerfaces

December 2015.

Ceccarelli M, Germani R, Massari S, Petit C, Nurisso A, Wolfender JL, Goracci L.

ARTICLE

Flavin monooxygenase metabolism: why medicinal chemists should matter

July 2014.

 Cruciani G, Valeri A,Goracci L, Pellegrino RM, Buonerba F, Baroni M

ARTICLE

Exposition and reactivity optimization to predict sites of metabolism in chemicals

Spring 2013

Cruciani G, Baroni M, Benedetti P, Goracci L, Fortuna CG

ARTICLE

High-throughput, computer assisted, specific MetID. A revolution for drug discovery

Spring 2013

Zamora I; Fontaine F; Serra B; Plasencia G

ARTICLE

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, 2013.

ARTICLE

Enhanced metabolite identification with MS(E) and a semi-automated software for structural elucidation.

November 2010.

Bonn B; Leandersson C; Fontaine F; Zamora I, 2010.

ARTICLE

CYP2C9 Structure−Metabolism Relationships:  Optimizing the Metabolic Stability of COX-2 Inhibitors

August 2007.

Ahlström MM, Ridderström M, Zamora I, Luthman K. J

ARTICLE

Comparison of methods for the prediction of the Metabolic sites for CYP3A4 – Mediated metabolic reactions

June 2006.

Diansong ZhouLovisa AfzeliusScott W. GrimmTommy B. AnderssonRandy J. Zauhar and Ismael Zamora

ARTICLE

MetaSite:  Understanding Metabolism in Human Cytochromes from the Perspective of the Chemist

September 2005.

Cruciani G, Carosati E, De Boeck B, Ethirajulu K, Mackie C, Howe T, Vianello R

ARTICLE

Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P450 2C9

June 2003.

Zamora, Ismael; Afzelius, Lovisa; Cruciani, Gabriele