Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores

•The first tool for dereplication of organic compounds from mass spectrometry imaging datasets•The software supports the standard imzML datafile format.•Dereplication can be performed also from conventional and LC-MS data formats.•De novo sequencing of nonribosomal peptide and polyketide siderophores is supported.•Nomenclature of linear and cyclic polyketide siderophores is proposed.

The open-source and cross-platform software CycloBranch was utilized for dereplication of organic compounds from mass spectrometry imaging imzML datasets and its functions were illustrated on microbial siderophores. The pixel-to-pixel batch-processing was analogous to liquid chromatography mass spectrometry data. Each data point represented here by accurate m/z values and the corresponding ion intensities was matched against integrated compound libraries. The fine isotopic structure matching was also embedded into CycloBranch dereplication process. The siderophores' characterization from single-pixel mass spectra was further supported by their de novo sequencing. New ketide building block library was utilized by CycloBranch to characterize the siderophores in images and mixtures and nomenclature of fragment ion series of linear and cyclic polyketide siderophores was proposed. The software is freely available at http://ms.biomed.cas.cz/cyclobranch. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.

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