title: Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores.
abstract: 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.
authors.affiliation: Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic. Electronic address: jiri.novak@biomed.cas.cz.
authors.forename: Jiří
authors.initials: J
authors.lastname: Novák
authors.affiliation: Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Lucie
authors.initials: L
authors.lastname: Sokolová
authors.affiliation: Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Lemr
authors.affiliation: Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Pluháček
authors.affiliation: Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Andrea
authors.initials: A
authors.lastname: Palyzová
authors.affiliation: Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic. Electronic address: vlhavlic@biomed.cas.cz.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Havlíček
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods; D061065:Polyketides / Q000737:chemistry*; D017262:Siderophores / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods
chemical_list: D061065:Polyketides; D017262:Siderophores
keywords: De novo sequencing; Dereplication; Desferri-coprogen (PubChem CID: 45479638); Desferri-ferricrocin (PubChem CID: 193746); Desferri-ferrioxamine B (PubChem CID: 2973); Desferri-ferrioxamine E (PubChem CID: 161532); Desferri-rhodotulic acid (PubChem CID: 29337); Desferri-triacetylfusarinin C (desferri-TAFC, PubChem CID: 6333736); Ferri-ferrioxamine B (PubChem CID: 123851); Ferri-triacetylfusarinin C (ferri-TAFC, PubChem CID: 6436274); Mass spectrometry imaging; Nonribosomal peptides; Polyketides; Siderophores