MSData

Dataset of mass spectra for R

Description and source

Intensity matrix from “Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli, Dryad, Dataset, https://doi.org/10.5061/dryad.bq64j”

The dataset was was downloaded from this link

Details

The file named RawIntensityMatrixChristner is a data.frame in .tsv format. The raw mass spectrum from to 891 strains were previously imported into the R environment. After signal processing with the MSclassifR package (using s/n = 2, tolerance = 0.002) and peaks detection (label = id_number), an intensity matrix was performed. This intensity matrix contained 891 rows (corresponding to the strains) and 1226 columns (corresponding to mass-over-charge (m/z)).

The file named MetadataShigatoxChristnermetadata is a .csv file associated to the intensity-matrix included 891 rows corresponding to the strains and 4 columns :

• Toxigenic_status: corresponding to the toxigenic status of the strain; according to the study:
  • norec: triplicate spectra from 190 non-outbreak related Escherichia coli isolates (189 clinical isolates collected during the time of the outbreak, reference strain DH5alpha)
  • orec: triplicate spectra from 104 outbreak related Escheriachia coli (O104:H4) isolates.
  • ref: triplicate spectra from three biological replicates of outbreak strain reference isolate TY-2482.
• id_number: corresponding to the number of the strain
• Strain_number: corresponding to the name of the strain in the study
• spot: corresponding to the plate spot for MALDI-TOF MS analysis
• type_of_extraction: type of extraction for MALDI-TOF MS analysis (only formic acid extraction was used (fae))

References

• Dataset:

Christner, Martin et al. (2015), Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli, Dryad, Dataset, https://doi.org/10.5061/dryad.bq64j

• Article:

Christner M, Trusch M, Rohde H, Kwiatkowski M, Schlüter H, et al. (2014) Rapid MALDI-TOF Mass Spectrometry Strain Typing during a Large Outbreak of Shiga-Toxigenic Escherichia coli. PLOS ONE 9(7): e101924. https://doi.org/10.1371/journal.pone.0101924

This site is open source. Improve this page.