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Aug212026

Table of Contents

OctoChemDB: A New Open-Source Platform for Small-Molecule Dereplication by HRMS

Metallic compounds, PeptidesAugust 21, 2026

By Ricardo Silvestre: Rapid dereplication of small molecules by high-resolution mass spectrometry (HRMS) relies on efficiently connecting experimental spectral data with information available across chemical databases. However, many existing databases provide limited support for direct m/z-based searches and integrated spectral analysis. To address this challenge, we developed OctoChemDB, an open-source platform that aggregates and harmonizes…

Aug52025

Mapping Binding Sites of Oxidovanadium Complexes on Angiotensin Peptides Using Tandem MS

Metallic compounds, PeptidesAugust 5, 2025

By Prof. Dr. Monika Cziferszky: Investigating the speciation of vanadium complexes in the presence of potential biomolecular targets under physiological conditions remains challenging and further experimental techniques are needed to better understand the mechanism of action of potential metallodrugs. A comprehensive analysis of the binding motifs between two model peptides (angiotensin I and angiotensin II)…

Apr302024

New cytotoxicity studies using Aom2s

Metallic compounds, Nucleic AcidsApril 30, 2024

By Jan Romano: Elucidating the molecular targets of metal drugs is crucial to shed light on their mechanism of action. In this study, Aom2s, a tool designed by scientists at EPFL to analyse HR-MS/MS spectra of oligonucleotides, was used to investigate the binding mode of a newly developed breast cancer drug candidate, [Ru(η6-toluene)(PPh3)2Cl]Cl, with single and double…

Dec22021

Designing anti-cancer metal complexes with the help of ms.tools

Proteins, Metallic compounds, Small moleculesDecember 2, 2021

By Alfonso Annunziata. The design of novel metallodrugs with improved biological characteristic is a hot topic in the fields of inorganic chemistry. In this work the synthesis and the structural characterization of novel platinum complexes with carbohydrate-derived ligands, to enhance the selectivity of the agents for cancer cells, was performed. The identity of the new…

Nov82021

A new vision for recycling plastics

Peptides, Polymers, ProteinsNovember 8, 2021

By Simone Giaveri: plastic pollution is one of the biggest issues that humanity has to face. Despite many efforts, a long-term solution for a sustainable handling, that is production and disposal, of synthetic polymer-based materials is still needed. At Prof. F. Stellacci’s lab, we envisioned a new circular-economy model for polymers, where materials are transformed…

Aug262021

New Protein-Binding studies using Apm2s

Metallic compounds, Peptides, ProteinsAugust 26, 2021

By Tao Jianmei. It is very important to study the protein-binding behavior of platinum drugs in blood. Mass spectrometry-based strategies have been used to identify and quantitate the proteins binding with platinum anticancer drugs in blood, as reviewed by Du et al in Pharmaceuticals. However, early attempts to identify the binding proteins of platinum drugs…

Sep232020

Aom2s: a new web‐based application for DNA/RNA data interpretation

Nucleic AcidsSeptember 23, 2020

We are happy to introduce our new RCMS publication about our recent addition to ms.epfl.ch toolbox: Aom2S. It was designed specifically for the automated analysis of oligonucleotide HR-MS/MS data. Aom2S offers the possibility to identify main type of fragments together with a-B ions, neutral losses, base losses and internal fragments. The assignment of all these product…

Jul92020

Metalloligands data treatment with ms.tools.epfl

Metallic compoundsJuly 9, 2020

By Erica Giraldi: The formation of triple-stranded helicates was first observed by high resolution ESI mass spectrometry. The functionalized helicates are attractive nanoscale building blocks for more complex supramolecular assemblies, as evidence by the synthesis of the largest trianglimine reported to date. Dominant peaks in the mass spectrum can be attributed to the trianglimine with…

Jun22020

ASMS Reboot 2020!

Peptides, Metallic compounds, Nucleic Acids, Polymers, Proteins, Small molecules, teachingJune 2, 2020

The ISIC-EPFL mass spectrometry platform team present a poster at the American society of mass spectrometry (ASMS2020) annual conference. Unfortunately, this year the Face-to-Face 68th ASMS Conference was cancelled due to the COVID-19 pandemic. Even if recording a talk is completely different from present a poster, we are excited to present this poster and video…

May202020

We love teaching !

Small molecules, teachingMay 20, 2020

Test the new exercises section on the ChemCalc website. They are generated randomly by means that every student has a different series (detailed statistics about the progression)! You don’t need any installation and no login is needed. Don’t forget to visit also our teaching section here.

Apr82020

Covid-19 collaboration with Stellacci’s group

Small moleculesApril 8, 2020

Our group is collaborating with the SUNMIL group (Prof. Francesco Stellacci’s group) to characterize potential drugs to fight against the COVID-19 pandemic. Check our last results collaboration published in Science advance last year.

Jan12020

Test the new chemcalc web page!

Metallic compounds, Peptides, Small moleculesJanuary 1, 2020

ChemCalc website, published back in 2012, received recently a new look that brings mobile device compatibility. This website allows among others to calculate monoisotopic mass and isotopic distribution as well as to find molecular formula from a monoisotopic mass.

Nov12019

The new polymer application MSPolyCalc was successfully tested.

PolymersNovember 1, 2019

As Desport et al cited in their publication, synthetic macromolecules consist of distributions of sizes, chemical compositions, functionalities and eventually architectures. MSPolyCalc could be an ideal MS tool for the data interpretation of this tremendous number of signals. Read the paper here

May12019

Study of Ionic Liquids as catalyst using soup of fragments

Small moleculesMay 1, 2019

Paul Dyson group describes how N‐formylation of amines with CO2 is base‐catalyzed. Moreover, studies of salt catalysts reveal that the reaction is efficiently catalyzed by “free” floating anions of high basicity, Martin used our free tool soup fragments to unravel the different ionic clusters formed in his experiments. Read details here

Apr82019

Cage or Prism?

Metallic compounds, Small moleculesApril 8, 2019

The newest publication of Giacomo Cecot (Prof. Kay Severin group) shows that Metal‐ligand assemblies of the general formula M8L4 can adopt prismatic or cage‐like structures. They have used our small molecule tools for their metallic characterization. Read the paper here

Feb12019

Aom2 gave critical insights about the metal-protein binding sites of Histidine

Metallic compounds, Nucleic Acids, Small moleculesFebruary 1, 2019

Second article in collaboration with Prof. Dyson group using Aom2s software. Designed, synthesized and studied by Lucinda Batchelor, a varying spacer lengths of a series heterobimetallic Ru-Au complexes have been evaluated using our mstooblox. Check the article in here.

Jun92018

Characterizing huge Pd-coordination cages!

Metallic compoundsJune 9, 2018

During this very productive collaboration with Suzanne Jansze (Prof. Severin team) we have characterize the largest palladium cages described to date (15KDa). We have use soup of fragments to identify the different Pd complexes formed under Cold-Spray Ionization. Check the article in here.

Oct92017

Unravelling Ubiquitin-Cisplatin interactions

Metallic compounds, ProteinsOctober 9, 2017

Aom2 was used for the first time to study the ubiquitin-Cisplatin interaction. Ronald Lee’s works show clearly that the metallodrug interactions with proteins are considerably more complex that one would think. The use of Aom2 was critical to identify the numerous species founded after CID. Read the article here.

Jun92017

Intricate structures of M2nLn structures soved with SoF

Metallic compoundsJune 9, 2017

First work of Giacomo Cecot (Prof. Severin team) using SoF to characterize the different metallic complexes observed during the MS experiments. This work describes experimentally and theoretically different aspects about metallasupramolecular geometries. Read the article in here.

May92013

First Cheminfo steps!

UncategorizedMay 9, 2013

Luc Patiny team describes a simple approach to develop chemical web services. In this first steps, the chemcalc project allows multiple MS calculations such as isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. Read the full paper here.