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24 results for “MALDI-TOF MS”
Supplementary files - Evaluation of MALDI-TOF MS technology in small ruminant milk adulteration using raw bovine milk
<p>The dataset is a part of Supplementary file for the manuscript:</p> <p><strong>Evaluation of MALDI-TOF MS technology in small ruminant milk adulteration using raw bovine milk</strong> by L. Rysova, P. Cejnar, O. Hanus, V. Legarova, J. Havlik, H. Nejeschlebova, I. Nemeckova, R. Jedelska, M. Bozik, submitted to <em>Journal of Dairy Science</em> (Manuscript ID JDS.2021-21396), Received October 8, 2021, Accepted January 31, 2022, Corresponding author: bozik@af.czu.cz, <a href="https://doi.org/10.3168/jds.2021-21396">https://doi.org/10.3168/jds.2021-21396</a></p> <p><strong>File 1:</strong> Detailed MALDI-TOF method description</p> <p><strong>File 2: </strong>Quantification of milk adulteration – calibration of the model Quantification of milk adulteration – calibration of the model</p> <p><strong>Table S1: </strong>Baseline characteristics of pure bovine milk which was used as an adulterant of caprine milk<strong> </strong></p> <p><strong>Table S2: </strong>Baseline characteristics of pure bovine milk which was used as an adulterant of ovine milk</p> <p><strong>Table S3: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using set A as the training set and set B as the test set.</p> <p><strong>Table S4: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using both, set A and set B , as the one training set and set C as the test set.</p> <p><strong>Table S5: </strong>Root mean squared error (RMSE) of predicted caprine and ovine adulterated milk samples using set AB as the training set and set C as the test set.</p> <p>In this version <strong>SD values in Table S2 were corrected</strong>.</p>
MALDI-TOF MS spectra data included in Dumolin et al. 2019
<p>MALDI-TOF MS and genome assembly data used for benchmarking of the SPeDE dereplication program.</p> <p> </p>
MS-UMG: MALDI-TOF Mass Spectra and Resistance Information on Antimicrobials from University Medical Center Göttingen
<p>During routine diagnostic procedures, we aggregated MALDI-TOF MS data of organisms isolated from clinical specimens from the University Medical Center Göttingen (UMG) in 2020 / 2021. We integrated these with corresponding antimicrobial susceptibility profiles. This amounted to 26,961 mass spectra and 26,961 corresponding metadata entries for the year 2020, and 50,381 mass spectra and 50,381 corresponding metadata entries for 2021, respectively. The dataset reflects 348 different species of bacterial and fungal organisms and 72 different antimicrobial susceptibility testing (AST) results.</p> <p> </p> <p>Please cite: </p> <div> <div>Effect of Data Heterogeneity in Clinical MALDI-TOF Mass Spectra Profiles on Direct Antimicrobial Resistance Prediction through Machine Learning</div> </div> <div><span><span><span>Youngjun</span> <span>Park</span></span>, <span><span>Michael</span> <span>Weig</span></span>, <span><span>Christine</span> <span>Noll</span></span>, <span><span>Oliver</span> <span>Bader</span></span>, <span><span>Anne-Christin</span> <span>Hauschild</span></span></span></div> <div><span>bioRxiv </span><span>2024.10.18.617592; </span><span><span>doi:</span> https://doi.org/10.1101/2024.10.18.617592</span></div>
Data from: Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and metabarcoding
<p>Nowadays, most biodiversity assessments involving meiofauna are mainly carried out using very time-consuming, specimen-wise morphological identifications, which demands comprehensive taxonomic knowledge. Animals have to be examined for minor differences of setae compositions, mouthpart morphology or number of segments for various extremities. DNA-based methods such as metabarcoding as well as recently emerged rapid analyses using MALDI-TOF mass spectrometry to identify specimens based on a proteome fingerprint could vastly accelerate the process of specimen identification in biodiversity assessments. However, these techniques depend on reference libraries to connect collected data to morphologically described species. In this study the success rate of both approaches have been tested based on reference libraries constructed using part of the samples from a new study area to identify unknown samples. Using MALDI-TOF MS we found, that species which do not exist in an incomplete mass spectra reference library only have minor impact on the results, when employing a post hoc test for Random Forest classifications. This test reveals specimens that demand morphological re-examination for the final species assignment. Metabarcoding however strongly demands a rich reference library to provide correct MOTU assessments in congruence with morphological determination. Nevertheless, with a complete library and a suitable data transformation [herein log(x + 1)], the number of reads per MOTU reflects relative species abundances in metabarcoding inference. The results of this study facilitate specimen identification by using MALDI-TOF MS, which is incomparably cheap for specimen-by specimen identification, but when it comes to sample-wise analyses, metabarcoding outperforms other techniques by far.</p>
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
<p>Cold-water corals build up reef structures or coral gardens and play an important role for many organisms in the deep sea. Climate change, deep-sea mining, and bottom trawling are severely compromising these ecosystems, making it all the more important to document the diversity, distribution, and impacts on corals. This goes hand in hand with species identification, which is morphologically and genetically challenging for Hexa- and Octocorallia. Morphological variation and slowly evolving molecular markers both contribute to the difficulty of species identification. In this study, a fast and cheap species delimitation tool for Octocorallia and Scleractinia of the Northeast Atlantic was tested based on 49 specimens. Two nuclear markers (ITS2 and 28S rDNA) and two mitochondrial markers (COI and mtMutS) were sequenced. The sequences formed the basis of a reference library for comparison to the results of species delimitation based on proteomic analysis using the MALDI-TOF MS method. The genetic methods were able to distinguish 17 of 18 presumed species. The MALDI-TOF MS method was able to distinguish 7 species. Species that could not be distinguished from one another still achieved good signals but were not represented by enough specimens for comparison. Therefore, it is predicted that with an extensive reference library of proteome spectra for Scleractinia and Octocorallia, MALDI-TOF MS may provide a rapid and cost-effective alternative for species discrimination in corals.</p>
Rapid pathogen identification in aqueous humor samples by combining Fc-MBL@Fe3O4 enrichment and MALDI-TOF MS profiling
<p>Prompt clinical diagnosis and antimicrobial therapy are key to managing infective endophthalmitis. The small volume of aqueous humor, low bacterial counts, and empirical medication by physicians make existing diagnostic methods time-consuming and imprecise. Here, we investigated the feasibility of combining Fc-MBL@Fe3O4 enrichment with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling to identify pathogens in aqueous humor. Aqueous humor aspirated from freshly enucleated porcine eyes was inoculated with different inocula of <em>Staphylococcus aureus</em> (<em>S. aureus</em>), <em>Staphylococcus </em><em>epidermidis</em> (<em>S. epidermidis</em>), and <em>Klebsiella pneumoniae</em> (<em>K. pneumoniae</em>). We performed identification directly in aqueous humor samples and after short-term culture of micro-LB broth. Aqueous humor endophthalmitis samples were enriched with Fc-MBL@Fe3O4 and analyzed with MALDI-TOF MS. The identification time and minimum bacterial concentration required for identification were determined. The enrichment efficiency of Fc-MBL@Fe3O4 for different bacteria was > (87.5±5.0)%. The objects of direct identification include live bacteria and bacteria treated with antibiotics, which can be completed within 1.5 hours. The minimum number of bacteria needed for positive identification was 2.20×10<sup>6 </sup>CFU. For micro-LB broth culture, the identification of bacteria can be completed within 6.5-9.5 h for aqueous humor samples with an initial bacterial count of tens to hundreds.</p>
MALDI-TOF MS spectra of archaeological whale bone specimens from Atlantic Europe
<p class="MsoNormal"><span>Whale bones are regularly found during archaeological excavations. Identification of these specimens to taxonomic levels is problematic due to their fragmented state. This lack of taxonomic resolution limits understanding of the past spatiotemporal distributions of whale populations and reconstructions of early whaling activities. To overcome this challenge, we performed Zooarchaeology by Mass-Spectrometry on an unprecedented selection of 719 archaeological and palaeontological specimens of probable whale bone from Atlantic European contexts, from the Middle to Late Neolithic (c.3500–2500 BCE) to the eighteenth century CE.</span></p> <p class="MsoNormal"><span>The results show high numbers of Balaenidae (most likely North Atlantic right whale (<em>Eubalaena glacialis</em>)) and grey whale (<em>Eschrichtius robustus</em>) specimens, two species no longer present in the eastern North Atlantic. Many of these specimens derive from contexts associated with the known medieval whaling cultures of the Basques, northern Spaniards, Normans, Flemish, Frisians, Anglo-Saxons, and Scandinavians. This association raises the likelihood that pre-industrial whaling impacted these taxa, contributing to their extinction and extirpation respectively. Much lower numbers of other large whale taxa were identified, suggesting that it was once abundant and accessible whales that suffered the greatest long-term impact. The pattern of natural abundance leading to over-exploitation, well-documented for other taxa, is thus applicable to early whaling. </span></p>
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
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Data from: Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and metabarcoding
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MALDI-TOF MS spectra of archaeological whale bone specimens from Atlantic Europe
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Machine learning in mass spectrometry: A MALDI-TOF MS approach to phenotypic antibacterial screening
<p>Dataset relating to the publication:</p> <p>Machine learning in mass spectrometry: A MALDI-TOF MS approach to phenotypic antibacterial screening</p> <p>by Luuk Nico van Oosten and Christian D. Klein</p> <p>Published in the Journal of Medicinal Chemistry, 2020</p> <p><strong>Important notice:</strong></p> <p><strong>The data are free to use for non-commercial, academic purposes, provided that the original source is<br> cited and the authors and the publication are credited in any derivative work.</strong></p> <p><strong>A patent application has been filed for the method described by van Oosten and Klein, which uses mass<br> spectrometry and machine learning to identify the pharmacological or other effects of compounds on cell<br> cultures and other biological systems.</strong></p> <p>Therefore, a license for the commercial use of the method must be negotiated by contacting either</p> <p>Anke Faller<br> Universität Heidelberg<br> Dezernat Forschung<br> Rechts- und Strukturfragen der Forschungsförderung<br> Seminarstraße 2, 69117 Heidelberg<br> Tel. +49 6221 54-12611<br> anke.faller(at)zuv.uni-heidelberg.de</p> <p>or</p> <p>Prof. Dr. C. Klein; c.klein(at)uni-heidelberg.de<br> Medicinal Chemistry<br> Institute of Pharmacy and Molecular Biotechnology IPMB<br> Heidelberg University, INF 364<br> D-69120 Heidelberg<br> Germany<br> Phone: ++49-6221-54-4875<br> FAX : ++49-6221-54-6430</p> <p> </p>
Data from: Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding
The North Sea is one of the most extensively studied marine regions of the world. Hence, large amounts of molecular data for species identification are available in public repositories, and expectations to find numerous new species in this well-known region are rather low. However, molecular reference data for harpacticoid copepods from this area in particular but also for this group in general is scarce. By assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans, it was discovered that there is a huge unknown diversity in this area. In total, COI sequences for 548 specimens from 115 species of harpacticoid copepods are presented. Over 19% of these were new to science and ten MOTUs were found to be part of cryptic species complexes. MALDI-TOF mass spectra were assessed for 622 specimens from 75 species. Because results were in concordance with species delimitation by COI barcoding and also enabled recognition of possible cryptic species, the discriminative power of this technique for biodiversity assessments is highlighted. Findings imply, species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.
Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
Background: Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. Results: Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. Conclusion: MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
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Data from: Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding
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Data from: Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS
<p>Quantifying spawning biomass of commercially relevant fish species is important to generate fishing quotas. This will mostly rely on the annual or daily production of fish eggs. However, these have to be identified precisely to species level to obtain a reliable estimate of offspring production of the different species. Because morphological identification can be very difficult, recent developments are heading towards application of molecular tools. Methods such as COI barcoding have long handling times and cause high costs for single specimen identifications. In order to test MALDI-TOF MS, a rapid and cost-effective alternative for species identification, we identified fish eggs using COI barcoding and used the same specimens to set up a MALDI-TOF MS reference library. This library, constructed from two different MALDI-TOF MS instruments, was then used to identify unknown eggs from a different sampling occasion. By using a line of evidence from hierarchical clustering and different supervised identification approaches we obtained concordant species identifications for 97.5% of the unknown fish eggs, proving MALDI-TOF MS a good tool for rapid species level identification of fish eggs. At the same time we point out the necessity of adjusting identification scores of supervised methods for identification to optimize identification success.</p>
MALDI-TOF MS spectra data included in Dumolin et al. 2021
<p>MALDI-TOF MS data from soil isolates dataset. </p>
MALDI-TOF MS spectra and sequence data of collagen of modern and archaeological flatfish from European waters
<p>MALDI-TOF MS spectra, LC-MS/MS datafiles, and Mascot MZID files of modern bone collagen of 18 species of Pleuronectiformes as reference spectra that were used to develop peptide biomarkers for ZooMS (Zooarchaeology by Mass Spectrometry). Details on the samples used can be found in the file "Reference spectra information.csv". Further information on the method and results can be found in the manuscript. The file names contain the type of data file and the species name. </p> <p>MALDI-TOF MS of 202 archaeological samples for Zooarchaeology by Mass Spectrometry (ZooMS) from three case study sites from around the North Sea: Barreau Saint-George ferroviaire in northern France, and 16-22 Coppergate and Blue Bridge Lane from York in the United Kingdom. Details on the samples can be found in the supplementary information of the manuscript. Further information on the method can be found in the manuscript. The file names are labeled with the sample ID number and the triplicate number (out of 3).</p>
MALDI-TOF MS spectra and sequence data of collagen of modern and archaeological flatfish from European waters
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Data from: Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS
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