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MicroMass Data Set
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Abstract: A dataset to explore machine learning approaches for the identification of microorganisms from mass-spectrometry data.

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Pierre Mahé, pierre.mahe '@', bioMérieux
Jean-Baptiste Veyrieras, jean-baptiste.veyrieras '@', bioMérieux

Data Set Information:

This MALDI-TOF dataset consists in:
A) A reference panel of 20 Gram positive and negative bacterial species covering 9 genera among which several species are known to be hard to discriminate by mass spectrometry (MALDI-TOF). Each species was represented by 11 to 60 mass spectra obtained from 7 to 20 bacterial strains, constituting altogether a dataset of 571 spectra obtained from 213 strains. The spectra were obtained according to the standard culture-based workflow used in clinical routine in which the microorganism was first grown on an agar plate for 24 to 48 hours, before a portion of colony was picked, spotted on a MALDI slide and a mass spectrum was acquired.
B) Based on this reference panel, a dedicated in vitro mock-up mixture dataset was constituted. For that purpose we considered 10 pairs of species of various taxonomic proximity:
* 4 mixtures, labelled A, B, C and D, involved species that belong to the same genus,
* 2 mixtures, labelled E and F, involved species that belong to distinct genera, but to the same Gram type,
* 4 mixtures, labelled G, H, I and J, involved species that belong to distinct Gram types.
Each mixture was represented by 2 pairs of strains, which were mixed according to the following 9 concentration ratios : 1:0, 10:1, 5:1, 2:1, 1:1, 1:2, 1:5, 1:10, 0:1. Two replicate spectra were acquired for each concentration ratio and each couple of strains, leading altogether to a dataset of 360 spectra, among which 80 are actually pure sample spectra.

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Relevant Papers:

Mahé et al. (2014). Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum. Bioinformatics.
Vervier et al., A benchmark of support vector machines strategies for microbial identification by mass-spectrometry data, submitted

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