Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28235 | ENA |
REPOSITORIES: ENA
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Project description:Whole-genome sequencing evaluation of MALDI-TOF MS as a species identification tool for Streptococcus suis
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Project description:Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing
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Project description:An improved MALDI-TOF MS data analysis pipeline for the identification of carbapenemase-producing Klebsiella pneumoniae
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Project description:To construct a rapid, high-throughput screening method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).
2021-07-21 | PXD027457 | iProX
Project description:It is of high importance to distinguish Tilletia caries and Tilletia laevis as causal agents of common bunt accurately from Tilletia controversa, the causal agent of dwarf bunt. All three of these wheat bunt diseases can lead to significant yield losses in crop production worldwide. But T. controversa is categorized as a quarantine pest in most areas of the world and must be discriminated from the T. caries / T. laevis complex. Usually, morphological characteristics of the teliospores are used to differentiate the three species. But due to natural hybridization and overlapping properties the discrimination is challenging. Germination behavior can also be considered for discrimination, but equivalent to their similar physiological and genetic traits the two agents of common bunt, T. caries and T. laevis could not be distinguished by this. It was suggested that the two species and maybe all three of those described Tilletia species might be conspecific. Up to now no molecular based method is available to differentiate the three species. Several studies have attempted the detection of the wheat bunt Tilletia species using PCR or other DNA-based methods. Other studies analyzed protein patterns with electrophoresis methods. But none of these approaches was able to distinguish between all of the three closely related Tilletia species. Several studies have shown that Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a useful tool to differentiate closely related fungal species. The aim of this study was to assess whether MALDI-TOF MS analysis is able to distinguish specimens of the three closely related pathogens T. caries, T. laevis, and T. controversa and may constitute an alternative method to the usually used morphology-based identification. Therefore MALDI-TOF MS was used to create subproteome fingerprints of the teliospores of 69 Tilletia specimens. These fingerprints were analyzed by comparing the mass spectra to each other by high-throughput multidimensional scaling (HiT-MDS ) together with hierarchical cluster analysis (HCA). The second approach was performed by discriminant analysis of principal components (DAPC). MALDI-TOF MS has proven to be a useful method for distinguishing between T. controversa and the two causal agents of common bunt, using our developed method of direct analysis of teliospores, but was unable to separate T. caries and T. laevis species. We conclude a potentially conspecific status of T. caries and T. laevis or even two morphotypes of one common species, causing identical disease symptoms and sharing the same germination requirements along with a related protein composition, shown in this study. Our developed MALDI-TOF MS method can be helpful in testing Tilletia bunt balls collected during field inspections, especially with regard to quarantine regulations or for breeding applications and may also be transferred to analyze further challenging sample material.
2022-02-14 | PXD030401 | Pride
Project description:Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has exhibited advantages in rapid analysis of metabolites. This data set provides support to the discuss of influence of interferential species, matrix effect and instrument parameters on metabolite qualification and quantification.
2021-12-28 | PXD030653 | iProX
Project description:Mass spectrometry (MS) based diagnostic detection of 2019 novel coronavirus infectious disease (COVID19) has been postulated to be a useful alternative to classical PCR based diagnostics. These MS based approaches have the potential to be both rapid, sensitive and can be done onsite without requiring a dedicated laboratory or depending on constrained supply chains (i.e., reagents and consumables). Matrix Assisted Laser Desorption Ionization (MALDI) time of flight (TOF) MS, has a long and established history of microorganism detection. Previously, we have shown that automated machine learning (ML) enhanced MALDI TOF MS diagnostics of nasal swabs can be both sensitive and specific for COVID19 detection. The underlying molecules responsible for this detection are generally unknown nor required for this automated ML platform to detect COVID19. However, the identification of these molecules is important for both understanding the diagnostic test itself and potentially the biology of the underlying infection. Here, we used nanoscale liquid chromatography tandem MS to identify endogenous peptides found in COVID19 positive anterior nares swab saline transport media to characterize mass over charge (m/z) values observed by the MALDI TOF MS method. We identified 14,270 endogenous peptides across 1,245 proteins groups that primarily comprise poly immunoglobulin receptor, actin, statherin, glyceraldehyde3phosphate dehydrogenase, basic salivary prolinerich protein 1 and histones. We also show that SARSCoV2 viral peptides were not readily detected and are highly unlikely to be responsible for the accuracy of MALDI based SARSCoV2 diagnostics.
2021-11-18 | MSV000088411 | MassIVE