Nucleic Acid‑MS Core Facility
The Nucleic Acid‑MS Core Facility at the MS Service Frankfurt specializes in the mass spectrometric analysis of nucleic acids and their chemical modifications. We provide advanced workflows for the detection, quantification, and structural analysis of modified nucleosides, oligonucleotides, and RNA fragments.
🔬 What We Offer
- MALDI-TOF MS of short oligonucleotides (<30 nts)
- Quantitative profiling of modified nucleosides (e.g., by NAIL-MS)
- High-resolution MS/MS analysis of synthetic and native oligonucleotides
- Fragmentation workflows (HCD, CID, ETD) for structural characterization
- Emerging workflows for shotgun RNomics (from 2025)
🧪 Instrumentation
- MALDI-TOF/TOF (Bruker Ultraflextreme) for short oligonucleotide n
- UHPLC-QQQ-MS (Agilent 6470) for targeted quantification
- HILIC LC for native RNA analysis
📄 Access & Request Process
Use of the Nucleic Acid-MS Core Facility is open to academic users upon request. Access is granted based on scientific merit, capacity, and project relevance. Priority is given to funded collaborations within SFB1309, TRR440, SCALE, and the Human RNome Project Consortium (HRPC).
To request access, please submit a scientific application (project abstract, sample type, number of samples). We will review your inquiry and assign an appropriate measurement slot. Applications should be submitted to Prof. Stefanie Kaiser
💰 Cost Model
For external or non-collaborative projects, the following rates apply:
- Nucleoside profiling: €25 per sample
- Oligonucleotide analysis: €50 per sample
All rates comply with DFG guidelines (Merkblatt 55.04) and cover preparation, measurement, and data handover. Quantitative analysis of nucleosides is possible if quantitative standards are provided to the Facility.
👥 Contact
- Scientific Lead: Prof. Dr. Stefanie Kaiser
- Technical Coordination: Leona Rusling (UHPLC-QQQ), Dr. Steffen Kaiser (MALDI-TOF)
- General Inquiries: Prof. Stefanie Kaiser
🌐 Related Projects
- SCALE – Cluster of Excellence
- SFB1309 – Chemical Biology of Epigenetic Modifications
- TRR440 – RNA Modifications in Structure and Regulation
- HRP – Human RNome Project Consortium
📚 Publications Using Our Facility
The Nucleic Acid-MS Core Facility has contributed to numerous high-profile publications through national and international collaborations. Below is a selection of recent work supported by our platform:
🔬 Nucleoside Mass Spectrometry
- With the Fu lab: Cell Reports, 2024
- With the Marschalek lab: Vaccine, 2025
- With the Stolz lab (SFB1177): Cell Reports, 2025
- With the Kowalinski lab: Nature Structural & Molecular Biology, 2024
- With the Blango lab: Nucleic Acids Research, 2024
🧬 Oligonucleotide MS (MALDI‑TOF)
→ If your work was supported by the Nucleic Acid-MS Core Facility and is not listed here, please contact us to be included.