ArticleJournal of the American Society for Mass Spectrometry2025
FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.
Article in Journal of the American Society for Mass Spectrometry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Activation of Oligonucleotide Polyanions Using Collisions, Electrons and Photons in a timsOmni Platform.Journal of the American Society for Mass Spectrometry · 2026Article
- Absorption Mode Broadband 2D MS for Proteomics and Metabolomics.Journal of the American Society for Mass Spectrometry · 2026Article
- Exploring RNA G-Quadruplex Stability in the Gas Phase: Insights from Native Mass Spectrometry.ChemPlusChem · 2026Article
- A Fast Neural Network for Isotopic Charge State Assignment.Journal of the American Chemical Society · 2025Article
- The intrinsic preference of guanosine bases for cleavage-facilitating interactions with phosphodiester moieties in RNA anions revealed by base modifications and mass spectrometry.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Top-down mass spectrometry (MS) enables comprehensive characterization of modified proteins and nucleic acids and, when native electrospray ionization (ESI) is used, binding site mapping of their complexes with native or therapeutic ligands. However, the high complexity of top-down MS spectra poses a serious challenge to both manual and automated data interpretation, even when the protein, RNA, or DNA sequence and the type of modification or the ligand are known. Here, we introduce FAST MS, a user-friendly software that identifies, assigns and relatively quantifies signals of molecular and fragment ions in MS and MS/MS spectra of biopolymers with known sequence and provides a toolbox for statistical analysis. FAST MS searches mass spectra for ion signals by comparing all signals in the spectrum with isotopic profiles calculated from known sequences, resulting in superior sensitivity and an increased number of assigned fragment ions compared to algorithms that rely on artificial monomer units while maintaining the false positive rate on a moderate level (<5%). FAST MS is an open-source, cross-platform software for the accurate identification, localization and relative quantification of modifications, even in complex mixtures of positional isomers of proteins, oligonucleotides, or any other user-defined linear polymer.
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Registered trials
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