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Label-free quantitative proteomics in Candida yeast species: technical and biological replicates to assess data reproducibility

Abstract : Objective: Label-free quantitative proteomics has emerged as a powerful strategy to obtain high quality quantitative measures of the proteome with only a very small quantity of total protein extract. Because our research projects were requiring the application of bottom-up shotgun mass spectrometry proteomics in the pathogenic yeasts Candida glabrata and Candida albicans, we performed preliminary experiments to (i) obtain a precise list of all the proteins for which measures of abundance could be obtained and (ii) assess the reproducibility of the results arising respectively from biological and technical replicates. Data description: Three time-courses were performed in each Candida species, and an alkaline pH stress was induced for two of them. Cells were collected 10 and 60 min after stress induction and proteins were extracted. Samples were analysed two times by mass spectrometry. Our final dataset thus comprises label-free quantitative prot-eomics results for 24 samples (two species, three time-courses, two time points and two runs of mass spectrometry). Statistical procedures were applied to identify proteins with differential abundances between stressed and unstressed situations. Considering that C. glabrata and C. albicans are human pathogens, which face important pH fluctuations during a human host infection, this dataset has a potential value to other researchers in the field. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/ publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Objective Studying proteome dynamics is a key step in systems biology projects. In this context, label-free bottom-up shotgun MS-based proteomics produces quantitative analyses of proteomes. This technique has emerged from significant improvements achieved by mass spectrom-etry (MS) instrumentation, chromatographic separation systems and a stronger correlation between the relative measured ion intensity and the original molecule abundance in the electrospray ionization process [1-3]. Members of our research team were involved in functional genomics studies in pathogenic yeasts Candida glabrata and Candida albicans [4-8]. We observed how the experimental design is a critical step to empower the statistics used to assess the robustness of the results. "How many replicates is enough?" is certainly one of the most frequently asked questions in wet laboratories. This question is especially critical in situations where the experiments are expensive, and/or the preparation of the biological samples is challenging. Here, our objective was to assess the robustness of the results arising from label-free bottom-up shotgun MS-based proteom-ics performed in C. glabrata and C. albicans, in case of technical and biological replicates. If the importance of biological replicates was indisputable when we started
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Submitted on : Monday, December 2, 2019 - 2:42:50 PM
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Gaëlle Lelandais, Thomas Denecker, Camille Garcia, Nicolas Danila, Thibaut Léger, et al.. Label-free quantitative proteomics in Candida yeast species: technical and biological replicates to assess data reproducibility. BMC Research Notes, BioMed Central, 2019, 12 (1), pp.470. ⟨10.1186/s13104-019-4505-8⟩. ⟨hal-02389332⟩

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