CEEPC/IPM/CMSC - Abstrakt prezentace

(CEEPC/IPM/CMSC 2022 - FrO-13)
Quantification of small molecules in liquid chromatography/mass spectrometry datasets by CycloBranch

Jiří Novák 1,2 *, Vladimír Havlíček 1

  1. Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 142 20 Prague 4
  2. Faculty of Information Technology, CTU in Prague, Thákurova 9, 160 00 Prague 6


CycloBranch (https://ms.biomed.cas.cz/cyclobranch/) is our open-source, cross-platform, and stand-alone tool originally dedicated to the analysis of accurate tandem mass spectra of cyclic and branched peptides [1]. Recently, the tool was extended to support the dereplication and de novo molecular formula determination of compounds in high-resolution conventional mass spectra, liquid chromatography/mass spectrometry (LC/MS) datasets, and imaging mass spectrometry datasets [2, 3]. Here, we show how the tool can be used for the quantification of small molecules in LC/MS data. For this purpose, the latest version of CycloBranch processes multiple LC/MS data files in a batch. Shapes of peaks in automatically constructed extracted ion chromatograms are approximated with Gaussian and exponentially modified Gaussian functions. If an input calibration dataset is available, CycloBranch calculates concentrations of compounds from the areas under chromatographic peaks upon an automated calibration curve construction. The tool supports the community standard mzML file format as well as several vendors’ native file formats. A custom database of compounds and a list of ion types to be found can be defined in a user-friendly graphical interface.

* Korespondující autor: jiri.novak@biomed.cas.cz


  1. Novák J. et al.: J. Am. Soc. Mass Spectrom. 26(10), 1780-1786 (2015).
  2. Novák J. et al.: Anal. Chem. 92(10), 6844-6849 (2020).
  3. Novák J. et al.: Chem. Listy 116(1), 11-19 (2022).


This work was supported by the Czech Science Foundation projects 21-17044S and 22-06771S.

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