Analysis of Microbial Siderophores by Mass Spectrometry

Quantitation of small molecules from liquid chromatography-mass spectrometric accurate mass datasets using CycloBranch

Gaussian and exponentially modified Gaussian functions were incorporated into integrating algorithms used by an open-source, cross-platform tool called CycloBranch. The quantitation is demonstrated on bacterial pyoverdines separated by fine isotope features. Using our algorithm, we can separate the m/z values 694.25802 and 694.26731 (a 0.009 Da difference), where the former belongs to the most intense peak of pyoverdine D (PvdD), and the latter to the second most intense peak of pyoverdine E (PvdE) in the respective isotopic clusters of [M + Fe-H]²⁺ ions. The areas under chromatographic curves of standards were analyzed for the limit of detection (LOD), limit of quantitation (LOQ), and regression coefficient calculations. The quantitative module returned a LOD and LOQ of 1.4 and 4.3 ng/mL, respectively, for both PvdD and PvdE in human urine. If present and detected in mass spectra, the intensities of user-defined [M + H]⁺, [M + Na]⁺, [M + K]⁺, [M + Fe-H]²⁺, or other ion types, can be accumulated and used for quantitation. The quantitation result is returned by CycloBranch in seconds or minutes, contrary to an hours-long manual approach, prone to user-born errors originating from necessary copying among various software environments. Native Bruker, Waters, Thermo, txt, mgf, mzML, and mzXML data formats are supported in CycloBranch, which is freely available at https://ms.biomed.cas.cz/cyclobranch.

MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis

Nonribosomal peptides and polyketides are natural products commonly synthesized by microorganisms. They are widely used in medicine, agriculture, environmental protection, and other fields. The structures of natural products are often analyzed by high-resolution tandem mass spectrometry, which becomes more popular with its increasing availability. However, the characterization of nonribosomal peptides and polyketides from tandem mass spectra is a nontrivial task because they are composed of many uncommon building blocks in addition to proteinogenic amino acids. Moreover, many of them have cyclic and branch-cyclic structures. Here, we introduce MassSpecBlocks – an open-source and web-based tool that converts the input chemical structures in SMILES format into sequences of building blocks. The structures can be searched in public databases PubChem, ChemSpider, ChEBI, NP Atlas, COCONUT, and Norine and edited in a user-friendly graphical interface. Although MassSpecBlocks can serve as a stand-alone database, our primary goal was to enable easy construction of custom sequence and building block databases, which can be used to annotate mass spectra in CycloBranch software. CycloBranch is an open-source, cross-platform, and stand-alone tool that we recently released for annotating spectra of linear, cyclic, branched, and branch-cyclic nonribosomal peptides and polyketide siderophores. The sequences and building blocks created in MassSpecBlocks can be easily exported into a plain text format used by CycloBranch. MassSpecBlocks is available online or can be installed entirely offline. It offers a REST API to cooperate with other tools.

Quantitative high-throughput approach to chalkophore screening in freshwaters

There is an increasing need to study the effects of trace metal micronutrients on microorganisms in natural waters. For Fe, small Fe-binding ligands called siderophores, which are secreted from cells and bind Fe with high affinity, have been demonstrated to modulate bioavailability of this critical nutrient. Relatively little is known about secretion of strong Cu-binding ligands (chalkophores) that may help organisms navigate the divide between Cu nutrition and toxicity. A barrier to environmental chalkophore research is a lack of literature on chalkophore analysis. Here we report the development of a quantitative, high-throughput approach to chalkophore screening based on a popular competitive-ligand binding assay for siderophores wherein ligands compete for metal in a chromogenic ternary complex of chrome azurol sulfonate-metal-surfactant. We developed the assay for high-throughput analysis using a microplate reader. The method performance is slightly better than that of comparable screening approaches for siderophores. We find that levels of other metals in natural samples may be capable of causing matrix interferences (a neglected source of analytical uncertainty in siderophore screening) and that for our method this can be overcome by standard additions. In this respect the high-throughput nature of the technique is a distinct advantage. To demonstrate practical use, we tested samples from field mesocosm studies that were set up with and without Cu and Fe amendments; we find trends in results that are logical in the environmental context of our application. This approach will be useful in areas such as risk assessment for a rapid survey of metal speciation and bioavailability; investigators who perform structural studies might also benefit from this approach to rapidly screen and select samples with high Fe/Cu binding capacity for further study.

Rhizoferrin Glycosylation in Rhizopus microsporus

Rhizopus spp. are the most common etiological agents of mucormycosis, causing over 90% mortality in disseminated infections. The diagnosis relies on histopathology, culture, and/or polymerase chain reaction. For the first time, the glycosylation of rhizoferrin (RHF) was described in a Rhizopus microsporus clinical isolate by liquid chromatography and accurate tandem mass spectrometry. The fermentation broth lyophilizate contained 345.3 ± 13.5, 1.2 ± 0.03, and 0.03 ± 0.002 mg/g of RHF, imido-RHF, and bis-imido-RHF, respectively. Despite a considerable RHF secretion rate, we did not obtain conclusive RHF detection from a patient with disseminated mucormycosis caused by the same R. microsporus strain. We hypothesize that parallel antimycotic therapy, RHF biotransformation, and metabolism compromised the analysis. On the other hand, the full profile of posaconazole metabolites was retrieved by our in house software CycloBranch.