Data availability
Data are freely available from the dedicated GitHub repository (https://github.com/michaelwitting/RepoRT). Source data are provided with this paper.
Code availability
All code is freely available from the dedicated GitHub repository (https://github.com/michaelwitting/RepoRT).
References
Héberger, K. J. Chromatogr. A 1158, 273–305 (2007).
Witting, M. & Böcker, S. J. Sep. Sci. 43, 1746–1754 (2020).
Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. & Neumann, S. J. Cheminformatics 8, 3 (2016).
Bach, E., Szedmak, S., Brouard, C., Böcker, S. & Rousu, J. Proc. European Conference on Computational Biology (ECCB 2018), i875–i883 (2018).
Harrieder, E.-M., Kretschmer, F., Böcker, S. & Witting, M. J. Chromatogr. B 1188, 123069 (2022).
Stanstrup, J., Neumann, S. & Vrhovšek, U. Anal. Chem. 87, 9421–9428 (2015).
Kimata, K. et al. J. Chromatogr. Sci. 27, 721–728 (1989).
Snyder, L. R., Dolan, J. W. & Carr, P. W. J. Chromatogr. A 1060, 77–116 (2004).
Kretschmer, F., Seipp, J., Ludwig, M., Klau, G. W. & Böcker, S. Preprint at bioRxiv https://doi.org/10.1101/2023.03.27.534311 (2023).
Domingo-Almenara, X. et al. Nat. Commun. 10, 5811 (2019).
Acknowledgements
F.K., M.A.H., and S.B. are supported by Deutsche Forschungsgemeinschaft (BO 1910/23). F.K. and S.B. are supported by the Ministry for Economics, Sciences and Digital Society of Thuringia (Framework ProDigital, DigLeben-5575/10-9). E.-M.H. and M.W. are supported by Deutsche Forschungsgemeinschaft (MW 4382/10-1). We thank everybody who publicly shared their retention time data. We thank J. Büscher for providing and uploading unpublished data. We express particular thanks to J. Stanstrup, who allowed us to integrate data from PredRet into RepoRT.
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Contributions
S.B. and M.W. designed the research. F.K., M.A.H., and M.W. implemented the repository. E.-M.H. manually curated datasets. F.K. and S.B. developed methods for automated error detection. E.-M.H. measured the systematically varying chromatographic parameters of the datasets. F.K. and M.A.H. implemented methods. E.-M.H. and M.W. performed a statistical analysis of the repository content. F.K., E.-M.H., S.B., and M.W. wrote the manuscript.
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Peer review information
Nature Methods thanks Joshua Rabinowitz and Juho Rousu for their contribution to the peer review of this work.
Supplementary information
Supplementary Information
Supplementary Notes 1–7, Supplementary Figs. 1–6, and Supplementary Tables 1, 4, 6 and 7
Supplementary Table 2
Tanaka parameters
Supplementary Table 3
Hydrophobic subtraction model parameters
Supplementary Table 5
Standard column names used in RepoRT
Source data
Source Data Fig. 1
Raw data for panels a,b,c,d,f
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Kretschmer, F., Harrieder, EM., Hoffmann, M.A. et al. RepoRT: a comprehensive repository for small molecule retention times. Nat Methods 21, 153–155 (2024). https://doi.org/10.1038/s41592-023-02143-z
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DOI: https://doi.org/10.1038/s41592-023-02143-z
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