Publication

Transient-mediated simulations of FTMS isotopic distributions and mass spectra to guide experiment design and data analysis

Résumé

Fourier transform mass spectrometry (FTMS) applications require accurate analysis of extremely complex mixtures of species in a wide mass and charge state ranges. To optimize the related FTMS data analysis accuracy, parameters for data acquisition and the allied data processing should be selected rationally and their influence on the data analysis outcome is to be understood. Thus, to facilitate this selection process and to guide the experiment design and data processing workflows, we implemented the underlying algorithms in a software tool with a graphic user interface, FTMS Isotopic Simulator. This tool accurate-ly computes FTMS data via time-domain data (transient) simulations for user-defined molecular species of interest and FTMS instruments, including diverse Orbitrap FTMS models, followed by user-specified FT processing steps. Herein we describe implementation and benchmarking of this tool for analysis of a wide range of compounds, as well as compare simulated and experimentally-generated FTMS data. In particular, we discuss the use of this simulation tool for narrowband and broadband, low- and high-resolution analysis of small mol-ecules, peptides and proteins, up to the level of their isotopic fine structures. By demonstrating the allied FT processing artifacts, we raise awareness of a proper selection of FT processing parameters for modern applications of FTMS, including intact mass analysis of proteoforms and top-down proteomics. Over-all, the described transient-mediated approach to simulate FTMS data has proven useful for supporting contemporary FTMS applications. We also find its utility in fundamental FTMS studies and creating didactic materials for FTMS teaching.

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Concepts associés (32)
Spectrométrie de masse
thumb|right|Spectromètre de masse La spectrométrie de masse est une technique physique d'analyse permettant de détecter et d'identifier des molécules d’intérêt par mesure de leur masse, et de caractériser leur structure chimique. Son principe réside dans la séparation en phase gazeuse de molécules chargées (ions) en fonction de leur rapport masse/charge (m/z). Elle est utilisée dans pratiquement tous les domaines scientifiques : physique, astrophysique, chimie en phase gazeuse, chimie organique, dosages, biologie, médecine, archéologie.
Tandem mass spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides. The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q).
Spectrométrie de masse à résonance cyclonique ionique
La spectrométrie de masse à résonance cyclotronique ionique (FT-ICR-MS) est un instrument possédant un haut pouvoir de résolution et une bonne exactitude sur la masse très important pour l’analyse des protéines. C’est une technique basée sur le piégeage et l’excitation des ions dans une cellule ICR (résonance cyclotronique des ions) sous l’action d’un champ électromagnétique. Le spectre de masse est obtenu via la transformée de Fourier qui convertit le signal temporel acquis en spectre de fréquence proportionnel à la masse.
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