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59 results for “MALDI-TOF”
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 mass spectrometry profiling of bovine skim milk for subclinical mastitis detection
<p>MALDI-TOF spectra acquired from bovine milk collected from dairy cows in Piedmont (Italy)</p>
iGEM Leiden 2023 - MALDI-TOF data for PHA identification
<p>Raw data of MALDI-TOF experiment aimed at identifying PHA in <em>Methylobacterium extorquens</em> AM1.</p>
MALDI-TOF MS spectra and sequence data of collagen of modern and archaeological flatfish from European waters
Open the record for dataset details and reuse information.
Data from: Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS
Open the record for dataset details and reuse information.
Brucker Maldi-TOF custom database for differentiating Enterococcus faecium clades A1/A2 from B
<p>This custom database has been constructed using MBT explorer software (Bruker ®) and the Maldi Biotyper (Bruker). Protein extraction were performed according to the MSP Creation protocol (V1.1, Bruker ®) and mass spectra were obtained following the Maldi Biotyper protocol (V.2.4, Bruker ®). The resulting spectra were carefully inspected using flexAnalysis software (V3.4, Bruker ®). After elimination of spectra with mass peak deviation > 0.05%, outlier peaks or flatline, the remaining spectra were combined to generate a single mass spectrum for each strain onto the MALDI Biotyper software (V4.1, Bruker ®), with default parameters. The mass spectra were used to generate this new database, available on the MBT Compass RUO software (RevC Version, Bruker ®). </p> <p>The individual spectra are available as well as the MSP (Mass Spectrum Profile) for each strains.</p>
SARS-CoV2 (COVID-19) Diagnosis in Human Saliva by MALDI-TOF MS Profiling
ClinicalTrials.gov study NCT04460638. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Screening and Therapeutic Monitoring of Multiple Myeloma by MALDI-TOF MS Analysis
ClinicalTrials.gov study NCT05686447. IPD Sharing: NO. Countries: 1. Publications: 0.
Research on Potential Biomarkers of Prediabetes and Diabetes Based on MALDI-TOF MS Platform.
ClinicalTrials.gov study NCT06097065. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Matrix Selection for the Visualization of Small Molecules and Lipids in Brain Tumors Using Untargeted MALDI-TOF Mass Spectrometry Imaging
GEO Series GSE279139. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Rapid Detection of Bacterial Resistance by MALDI-TOF MS and Antibiotic Savings
ClinicalTrials.gov study NCT02860247. IPD Sharing: NO. Countries: 0. Publications: 0.
MALDI-TOF spectra of Clostridioides difficile Ribotypes
<p>MALDI-TOF spectra of different ribotypes of Clostridioides difficile. Cultured anaerobically on Brucella Blood agar after 48 hours at 37ºC. <br>Acquisition on MBT Smart MALDI Biotyper (Bruker Daltonics). </p> <p>Version 2 (correction on folder organization)</p>
Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry)
<p><strong>Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry)</strong></p> <ul> <li>This data set originates from a collection of 41 clinical strains of <em>Mycobacterium abscessus complex</em> corresponding to 1001 mass spectra: <ul> <li>25 strains of <em>Mycobacterium abscessus</em> subsp. <em>abscessus</em> (633 mass spectra)</li> <li>9 strains of <em>Mycobacterium abscessus</em> subsp. <em>massiliense</em> (204 mass spectra)</li> <li>7 strains of <em>Mycobacterium abscessus</em> subsp. <em>bolletii </em>(164 mass spectra)</li> </ul> </li> </ul> <p> </p> <ul> <li>Each strain has been characterized using molecular method (DNA/DNA hydridation, using GenoType NTM-DR (Hain Lifescience, Nehren, Germany) according to the manufacturer's instructions for identification and analyzed by MALDI-TOF mass spectrometry according MycoEx protocol (Bruker<sup>®</sup>). The mass spectra spectra were obtained according to the following steps :</li> </ul> <p> </p> <ol> <li>Each of the 41 strains was cultured in aerobic atmosphere at 37°C for 7 ± 2 days on blood agar (COH, bioMerieux<sup>®</sup>). Then, one colony was extracted according to the MycoEx protocol (Bruker<sup>®</sup>). For each of the extracts, 8 technical replicates were realized and analyzed by MALDITOF MS (Bruker<sup>®</sup>). Dried spots were overlaid with 1µL of MALDI matrix (α-HCCA).</li> <li> <p>Data acquisition was performed using a Microflex LT (Bruker<sup>®</sup> Daltonics) mass spectrometer equipped with a N2 laser (λ =377 nm). Instrument parameters used were as follows: a masse range between 200-20000 Da, ion source 1: 20 kV, ion source 2: 18.5 kV, Iens: 8.45 kV, pulsed ion extraction: 330 ns, laser frequency: 20.0 Hz. Spectra were obtained after 500 shots. Each spot was analyzed three times. In total 24 spectra were obtained for each extraction.</p> </li> <li> <p>Spectra acquired for each isolate were visualized and analyzed using Flex Analysis software (Bruker<sup>®</sup> Daltonics), and spectra with low quality peaks were removed. A minimum of 15 spectra per extraction was necessary to validate the extraction.</p> </li> </ol> <p><strong>This database is only intended for medical research. Please contact: medecine-drv@sorbonne-universite.fr for data access.</strong></p> <p>After access agreement, the three following files will be available :</p> <ul> <li>The MABSC_spectra.zip file contains the MS peak list data in a Matlab compatible format.</li> <li>The MABSC_metadata.pdf file contains the molecular identifications of strains.</li> <li>The MABSC_notes.txt file contains informations concerning contains informations on the method of obtaining the data.</li> </ul>
MALDI-TOF spectra and bone images of archaeological and modern European Cyprinids
<p>Images from all 46 archaeological test bones associated with the archaeological test set MALDI-TOF data.</p> <p>MALDI-TOF data from both reference and test sets. Reference sets are labeled with their species identification. Each set consists of .tex files. Files in the same folder are technical replicates of the same extract.</p>
Spectra from "Contribution of MALDI-TOF mass spectrometry and Machine Learning including Deep Learning techniques for the detection of virulence factors of Clostridioides difficile strains"
<p><strong>This database includes spectra from 201 <em>C. difficile </em> (CD) strains :</strong></p> <ul> <li>50 non-toxigenic strains (tcdA- tcdB-) (designated ToxA-B-) belonging to 19 different PR,</li> <li>151 toxigenic strains harbouring toxins A and B genes (ToxA+B+). Among the 151 ToxA+B+ strains, 46 corresponding to 8 different PR also harboured the binary toxin genes (ToxA+B+CDT+) and 105 (23 different PR) did not (ToxA+B+CDT-).</li> <li>Among the 46 ToxA+B+CDT+ strains, 22 belonged to the Hv strains i.e. PR 027 (n=13), PR 176 (n=5) and PR 181 (n=4) strains (ToxA+B+CDT+Hv) (Table S1). </li> </ul> <p><strong>Sample preparation.</strong> Each isolate stored at −80°C (Microbank; Pro-Lab Diagnostics) was thawed and cultivated on Columbia Blood Agar (CBA, bioMérieux) incubated in anaerobic atmosphere at 37°C for 48 hours. A subculture was performed in the same conditions. A chemical protein extraction was then carried out. Briefly, a single colony was suspended in 200 µl water and vortexed. After adding 900 µl ethanol, samples were vortexed and centrifuged at 13,000 × g for 2 minutes. The supernatant was removed, and the remaining ethanol was evaporated at room temperature. Next, 25 µl of 70% formic acid was added and mixed with the pellet, then 25 µl of acetonitrile was added. After centrifugation at 13,000 × g for 2 minutes, the supernatant was ready for analysis. <strong>Eight deposits were performed for each isolate.</strong> The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and <strong>each spot was analysed three times by MALDI-TOF MS</strong>.</p> <p><br> <strong>MALDI-TOF MS acquisition and analysis.</strong> Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics).</p> <p><br> <strong>A total of 4659 spectra were produced. </strong></p> <p><strong>Fore more details: please contact alexandre.godmer@aphp.fr</strong><br> </p>
Spectral database of Streptococcus pneumoniae, S. mitis and S. pseudopneumoniae (MALDI-TOF Mass Spectrometry)
<p>A total of 80 strains, including 60 <strong>pneumococca</strong>l strains, 8 <strong><em>S. pseudopneumoniae</em> </strong>strains, and 12 <strong><em>S. mitis</em></strong> strains, were molecularly characterized and obtained from the National Reference Center for Pneumococci for the creation of the database. Each strain was tested a minimum of 20 and a maximum of 24 times using MALDI-TOF MS.</p> <p><br> MALDI-TOF MS acquisition and analysis. Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics). <strong>Eight deposits were performed for each isolate.</strong> The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and <strong>each spot was analysed three times by MALDI-TOF MS</strong>.</p> <p><strong>A total of 1890 spectra were produced :</strong></p> <ul> <li><em>S. mitis</em> (n=264),</li> <li><em>S.pneumoniae</em> (n= 1434),</li> <li><em>S. pseudopneumoniae </em>(n=192)</li> </ul> <p><strong>Fore more details:</strong> please contact alexandre.godmer@aphp.fr</p>
How to Get Your Goat: Automated Identification of Species from MALDI-ToF Spectra - MALDI-ToF dataset
<p>MALDI-ToF dataset relating to the journal article "How to Get Your Goat: Automated Identification of Species from MALDI-ToF Spectra" in <em>Bioinformatics</em>.</p>
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OpenNeuro
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