Abstract
Orbitrap-based charge detection mass spectrometry utilizes single-molecule sensitivity to enable mass analysis of even highly heterogeneous, high-mass macromolecular assemblies. For contemporary Orbitrap instruments, the accessible ion detection (recording) times are maximally ~1–2 s. Here by modifying a data acquisition method on an Orbitrap ultrahigh mass range mass spectrometer, we trapped and monitored individual (single) ions for up to 25 s, resulting in a corresponding and huge improvement in signal-to-noise ratio (×5 compared with 1 s), mass resolution (×25) and accuracy in charge and mass determination of Orbitrap-based charge detection mass spectrometry.
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Data availability
Raw transient data are publicly available on the MassIVE repository under accession code MSV000093797 (https://doi.org/10.25345/C5H41JZ1K). Source data are provided with this paper.
Code availability
A Python library, Jupyter notebook and representative dataset for processing of transient data are available as Supplementary Code.
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Acknowledgements
We acknowledge support from the Netherlands Organization for Scientific Research (NWO) funding the Netherlands Proteomics Centre through the X-omics Road Map program (project 184.034.019). A.J.R.H. acknowledges further support by NWO through the Spinoza Award SPI.2017.028. A.D.R. acknowledges support by an EMBO long-term fellowship (ALTF_371-2022). Y.O.T. acknowledges support from the European Horizon 2020 research and innovation program under grant agreement #964553 (ARIADNE). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
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Contributions
E.D., V.C.Y., E.H.T.M.E. and A.D.R. contributed to preliminary experimental work on ultralong transients. E.D. and V.C.Y. performed the experiments shown in the manuscript. A.B. provided technical support for DAQ on the Booster and Orbitrap. T.P.W. wrote the scripts for ultralong transient analysis, with further modifications from V.C.Y., E.D. and E.H.T.M.E. E.D., V.C.Y. and E.H.T.M.E. processed the data. K.L.F. modified the UHMR Orbitrap software and developed the ion pulse scheme to enable the acquisition of ultralong transients. K.O.N., A.N.K. and Y.O.T. installed the Booster and helped for processing of Booster data. A.A.M. and K.L.F. advised on the operation of the Orbitrap system and mechanisms in the Orbitrap analyzer at longer transients. V.C.Y. and A.J.R.H. supervised the study. A.J.R.H. conceived the project and acquired funding. E.D., V.C.Y. and A.J.R.H. drafted the manuscript. All authors provided critical feedback on the manuscript.
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The authors declare the following financial interests that may be considered as potential competing interests: three authors (K.L.F., T.P.W. and A.A.M.) are employees of Thermo Fisher Scientific, the manufacturer of the Orbitrap mass spectrometer used in the study, and three authors (A.N.K., K.O.N. and Y.O.T.) are employees of Spectroswiss, the manufacturer of the FTMS Booster X2 used in the study. The remaining authors declare no competing interests.
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Nature Methods thanks Justin Benesch, Kallol Gupta and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editor: Arunima Singh, in collaboration with the Nature Methods team.
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Supplementary information
Supplementary Information
Supplementary Figs. 1–10.
Supplementary Code
Python library, Jupyter notebook and representative dataset for ultralong transient processing.
Supplementary Data 1
Source data for Supplementary Figs. 1–10.
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Source Data Fig. 1
Statistical source data.
Source Data Fig. 2
Statistical source data.
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Deslignière, E., Yin, V.C., Ebberink, E.H.T.M. et al. Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry. Nat Methods 21, 619–622 (2024). https://doi.org/10.1038/s41592-024-02207-8
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DOI: https://doi.org/10.1038/s41592-024-02207-8
