Resource Library

MARS: A Multipurpose Software for Untargeted LC–MS-Based Metabolomics and Exposomics

January 18, 2024

Laura Goracci*, Paolo Tiberi, Stefano Di Bona, Stefano Bonciarelli, Giovanna Ilaria Passeri, Marta Piroddi, Simone Moretti, Claudia Volpi, Ismael Zamora and Gabriele Cruciani

Development of a Predictive Multiple Reaction Monitoring (MRM) Model for High-Throughput ADME Analyses Using Learning-to-Rank (LTR) Techniques

November 28, 2023.

Ramon Adalia, Shivani Patel, Anthony Paiva, Tierni Kaufman, Ismael Zamora, Xianmei Cai, Gemma Sanjuan, Wilson Z. Shou*

MassChemSite for In-Depth Forced Degradation Analysis of PARP Inhibitors Olaparib, Rucaparib, and Niraparib

February 2023

Stefano Bonciarelli, Jenny Desantis, Simone Cerquiglini, Laura Goracci 

Guiding the choice of informatics software and tools for lipidomics research applications

February 2023.

Zhixu Ni , Michele Wölk, Geoff Jukes, Karla Mendivelso Espinosa, Robert Ahrends, Lucila Aimo, Jorge Alvarez-Jarreta, Simon Andrews, Robert Andrews, Alan Bridge, Geremy C Clair, Matthew J Conroy, Eoin Fahy, Caroline Gaud, Laura Goracci, Jürgen Hartler, Nils Hoffmann, Dominik Kopczyinki, Ansgar Korf, Andrea F Lopez-Clavijo, Adnan Malik, Jacobo Miranda Ackerman, Martijn R Molenaar, Claire O’Donovan, Tomáš Pluskal, Andrej Shevchenko, Denise Slenter, Gary Siuzdak, Martina Kutmon, Hiroshi Tsugawa, Egon L Willighagen, Jianguo Xia, Valerie B O’Donnell, Maria Fedorova

Software and Computational Tools for LC-MS-Based Epilipidomics: Challenges and Solutions

January 2023.

Tito Damiani, Stefano Bonciarelli, Gerhard G Thallinger, Nikolai Koehler, Christoph A Krettler, Arif K Salihoğlu, Ansgar Korf, Josch K Pauling, Tomáš Pluskal, Zhixu Ni, Laura Goracci

A platelet lipidomics signature in patients with COVID-19

December 2023.

Laura Goracci, Eleonora Petito, Alessandra Di Veroli, Emanuela Falcinelli, Caterina Bencivenga, Elisa Giglio, Cecilia Becattini, Edoardo De Robertis, Gaetano Vaudo, Paolo Gresele

Analysis of Phosphatidylinositol Modifications by Reactive Nitrogen Species Using LC-MS: Coming to Grips with Their Nitroxidative Susceptibility

July 2023.

Stefano Bonciarelli, Bruna Neves, Pedro Domingues, Tânia Melo, Laura Goracci, Maria Rosário Domingues

Analytical and computational workflow for in-depth analysis of oxidized complex lipids in blood plasma

November 2022

Angela Criscuolo, Palina Nepachalovich, Diego Fernando Garcia-Del Rio, Mike Lange, Zhixu Ni, Massimo Baroni, Gabriele Cruciani, Laura Goracci, Matthias Blüher , Maria Fedorova

Retinoic acid-induced 1 gene haploinsufficiency alters lipid metabolism and causes autophagy defects in Smith-Magenis syndrome

November 2022

Elisa Maria Turco, Angela Maria Giada Giovenale, Laura Sireno, Martina Mazzoni, Alessandra Cammareri, Caterina Marchioretti, Laura Goracci, Alessandra Di Veroli, Elena Marchesan, Daniel D’Andrea, Antonella Falconieri, Barbara Torres, Laura Bernardini, Maria Chiara Magnifico, Alessio Paone, Serena Rinaldo, Matteo Della Monica, Stefano D’Arrigo, Diana Postorivo, Anna Maria Nardone, Giuseppe Zampino, Roberta Onesimo, Chiara Leoni, Federico Caicci, Domenico Raimondo, Elena Binda, Laura Trobiani, Antonella De Jaco, Ada Maria Tata, Daniela Ferrari, Francesca Cutruzzolà, Gianluigi Mazzoccoli, Elena Ziviani, Maria Pennuto, Angelo Luigi Vescovi, Jessica Rosati 

Oligonucleotides: degradation studies

70th ASMS Conference on Mass Spectrometry. June 2022

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

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

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

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora; Ramon Adàlia; Tatiana Radchenko

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

Improving metabolite identification for complex peptides using MassMetaSite

70th ASMS Conference on Mass Spectrometry. June 2022

Ismael Zamora; Tatiana Radchenko; Fabien Fontaine; Albert Garriga

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

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)

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)

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*

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 Koster, Ron.M.A. Heeren, Howard W. Clark, Anthony D. Postle 

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

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. 

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  

Phospholipidome of extra virgin olive oil: Development of a solid phase extraction protocol followed by liquid chromatography-high resolution mass spectrometry for its software-assisted identification

April 2020.

Antonelli M, Benedetti B, Cavaliere C, Cerrato A, Montone CM, Piovesana S, Lagana A, Capriotti AL.

New insights in hemp chemical composition: a comprehensive polar lipidome characterization by combining solid phase enrichment, high-resolution mass spectrometry, and cheminformatics

January 2020.

Antonelli M, Benedetti B, Cannazza G, Cerrato A, Citti C, Montone CM, Piovesana

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;

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.

Metabolite Identification Using An Ion Mobility-Enhanced Data-Independent Acquisition Strategy and Automated Data Processing.  Rapid Commun Mass Spectrom. 

Radchenko T; Kochansky CJ; Cancilla M; Wrona MD; Mortishire-Smith RJ; Kirk J; Murray G; Fontaine F; Zamora I.

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

Dissipation kinetic studies of fenamidone and propamocarb in vegetables under greenhouse conditions using liquid and gas chromatography coupled to high-resolution mass spectrometry

Chemosphere 226:36-46. 2019

López-Ruiz R; Romero-González R; Serra B; Garrido Frenich A

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

Dissipation studies of famoxadone in vegetables under greenhouse conditions using liquid chromatography coupled to high-resolution mass spectrometry: putative elucidation of a new metabolite

September 2019.

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

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. 

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.

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.

Software-aided workflow for predicting protease-specific cleavage sites using physicochemical properties of the natural and unnatural amino acids in peptide-based drug discovery

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

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 

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.

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

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 

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

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 

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.

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 

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.

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

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 

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. 

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. 

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.

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.

Metabolism study and biological evaluation of bosentan derivatives 

October 2016

Susan Lepri, Laura Goracci, Aurora Valeri, Gabriele Cruciani

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.

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 

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.

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 

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 

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. 

Software-aided structural elucidation in drug discovery

November 2015.

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

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.

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, 2014. 

Flavin monooxygenase metabolism: why medicinal chemists should matter

July 2014.

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

Exposition and reactivity optimization to predict sites of metabolism in chemicals

Spring 2013

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

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, 2013.

Update on hydrocodone metabolites in rats and dogs aided with a semi-automatic software for metabolite identification Mass-MetaSite

April 2013

Li AC; Chovan JP; Yu E; Zamora I, 2013.

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.

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

August 2007.

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

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

June 2006.

Diansong Zhou, Lovisa Afzelius, Scott W. Grimm, Tommy B. Andersson, Randy J. Zauhar and Ismael Zamora

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

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

June 2003.

Zamora, Ismael; Afzelius, Lovisa; Cruciani, Gabriele