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Peer-reviewedCC BYAnalytical chemistry

SpectrSeqTools: LC-MS/MS-Based De Novo Sequencing of Small Ribonucleic Acids with Post-Transcriptional Modifications.

  • Laura C Kühle1,2
  • Moshir Harsh1,3
  • Shanice Jessica Hermon1,3
  • Juan Magalang1,3
  • Johannes Köster2,4
  • Sidney Becker1,3
4 affiliations
  1. 1Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11, 44227Dortmund, Germany.
  2. 2Bioinformatics and Computational Oncology, Institute for AI in Medicine (IKIM), Faculty of Medicine, University Hospital Essen, University of Duisburg-Essen, Girardetstraße 2, 45131Essen, Germany.
  3. 3Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44227Dortmund, Germany.
  4. 4German Cancer Consortium (DKTK), University Hospital Essen, Hufelandstraße 55, Essen45147, Germany.
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Abstract

Post-transcriptional RNA modifications are key regulators of fundamental cellular processes. Yet, their precise biological functions remain largely unresolved. A major challenge is their reliable detection. While sequencing-based approaches are limited to a small subset of RNA modifications, mass spectrometry has the potential to directly identify various modified nucleotides within their sequence context. However, existing tools for nucleic acid analysis offer severely constrained functionality. Here, we introduce a set of algorithmic innovations implemented in SpectrSeqTools, an open-source LC-MS/MS-based software platform that enables fully automated de novo RNA sequencing together with comprehensive modification profiling of short RNA fragments directly from raw data. We further validated prediction accuracy and robustness using experimental and simulated data. As such, SpectrSeqTools effectively broadens the scope of nucleic acid mass spectrometry, enabling the read-out of up to 144 RNA modifications within their sequence context.

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Cite

BibTeXRIS
BibTeX
@article{kuhle2026spectrseqtools,
  title = {{SpectrSeqTools: LC-MS/MS-Based De Novo Sequencing of Small Ribonucleic Acids with Post-Transcriptional Modifications.}},
  author = {Laura C Kühle and Moshir Harsh and Shanice Jessica Hermon and Juan Magalang and Johannes Köster and Sidney Becker},
  journal = {Analytical chemistry},
  year = {2026},
  month = oct,
  doi = {10.1021/acs.analchem.6c02546},
  url = {https://europepmc.org/article/MED/42915714},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - SpectrSeqTools: LC-MS/MS-Based De Novo Sequencing of Small Ribonucleic Acids with Post-Transcriptional Modifications.
AU  - Laura C Kühle
AU  - Moshir Harsh
AU  - Shanice Jessica Hermon
AU  - Juan Magalang
AU  - Johannes Köster
AU  - Sidney Becker
PY  - 2026
DA  - 2026/10/01
JO  - Analytical chemistry
DO  - 10.1021/acs.analchem.6c02546
UR  - https://europepmc.org/article/MED/42915714
AB  - Post-transcriptional RNA modifications are key regulators of fundamental cellular processes. Yet, their precise biological functions remain largely unresolved. A major challenge is their reliable detection. While sequencing-based approaches are limited to a small subset of RNA modifications, mass spectrometry has the potential to directly identify various modified nucleotides within their sequence context. However, existing tools for nucleic acid analysis offer severely constrained functionality. Here, we introduce a set of algorithmic innovations implemented in SpectrSeqTools, an open-source LC-MS/MS-based software platform that enables fully automated de novo RNA sequencing together with comprehensive modification profiling of short RNA fragments directly from raw data. We further validated prediction accuracy and robustness using experimental and simulated data. As such, SpectrSeqTools effectively broadens the scope of nucleic acid mass spectrometry, enabling the read-out of up to 144 RNA modifications within their sequence context.
SN  - 0003-2700
SN  - 1520-6882
ER  -