Elsevier

Journal of Proteomics

Volume 213, 20 February 2020, 103619
Journal of Proteomics

MALDI TOF MS-profiling: Applications for bacterial and plant sample differentiation and biological variability assessment

https://doi.org/10.1016/j.jprot.2019.103619Get rights and content

Highlights

  • MALDI-Profiling offers an inexpensive, rapid and reliable approach for investigating protein profiles

  • MALDI-TOF MS can be used for protein profile differentiation of diverse samples, including bacteria as well as plants.

  • MALDI-TOF MS Profiling can aid in the analysis of samples regarding differential protein profile and experimental variability prior to more complex approaches including transcriptomics and proteomics.

Abstract

In this study, we evaluated the potential use of MALDI-TOF MS Profiling for the differentiation of biological samples submitted to different treatments. We compared the bacterium Xanthomonas campestris pv. campestris (Xcc), grown in culture medium and in vivo (recovered from the plant). Plant samples were also analyzed and included explants at different somatic embryogenesis (SE) stages, as well as leaves from Brassica oleracea and Arabidopsis thaliana inoculated with Xcc, at different time points. The results showed that bacteria and highly divergent plant samples, such as those from embryogenic stages, can be unequivocally differentiated and the clustering was in accordance with proteomic analysis performed by 2-DE. These results show an important application of MALDI-TOF MS Profiling to select and prioritize samples to be analyzed prior to more complex approaches including transcriptomics and proteomics. We also show that in plant-pathogen interactions, when more subtle differences are obtained, the main contribution of MALDI-TOF MS Profiling is in the assessment of experimental variability. This is relevant since reproducibility is a challenging issue when dealing with complex experimental conditions such as plant-pathogen interactions. We propose the use of MALDI-TOF MS Profiling to aid researchers in minimizing experimental variability unrelated to the condition being analyzed.

Significance

MALDI-Profiling offers an inexpensive, rapid and reliable approach for investigating the protein profile to assess sample differentiation and experimental variability in microorganisms and plants and can be highly useful to analyze samples prior to more complex and expensive techniques such as proteomics and transcriptomics.

Introduction

Important advances in mass spectrometry and data analysis softwares have been achieved in the past few years, allowing important contributions for scientific development in different areas. MALDI-TOF MS (Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry) is a powerful technique to achieve protein and peptide fingerprints. In the last decade, studies have shown the use of mass spectrometry for the identification of bacteria by combining MALDI-TOF MS with a software containing a protein profile database and comparison algorithms, which allows the identification of microorganisms in the species level [[1], [2], [3]]. Since then, MALDI-TOF MS Profiling (MALDI-Profiling) has been used to identify several microorganisms, including Gram-positive and Gram-negative bacteria [[4], [5], [6]]. The main application of this technique is for bacterial identification in clinical samples and has been routinely used for this purpose [[7], [8], [9]]. There are few studies reporting the use of this method aiming at the identification of microorganisms of environmental importance, such as plant-interacting bacteria or fungi [10,11].

Previously, we published a short review and perspective paper discussing the visionary applications of MALDI-Profiling in sample differentiation [12]. In the current work, we show a large amount of experimental data achieved from analyses of several biological samples, mainly plant-derived materials, and demonstrate that MALDI MS protein profiling is a powerful method for sample differentiation, as well as for biological variability assessment among experimental treatments.

Section snippets

Xanthomonas campestris pv. campestris grown in vitro and in vivo

We used the bacterium Xanthomonas campestris pv. campestris (Xcc), isolate Xcc 51, obtained from the culture collection of Embrapa Hortaliças-CNPH, Brazil. Xcc was cultured in vitro in the rich medium Nutrient Yeast Glycerol (NYG) according to Daniels et al. [13]. In vivo samples were obtained by recovering Xcc from the host plant Brassica oleracea susceptible (Kenzan) to Xcc, according to Mehta & Rosato [14], with some modifications. B. oleracea leaves were inoculated with Xcc (OD = 0.6) and

Results and discussion

The results obtained in this study revealed an important and novel application of MALDI-Profiling; we show that this technique can be used for protein profile differentiation of diverse samples, including bacteria as well as plants.

Initially, we compared the protein profile of the bacterium X. campestris pv. campestris (Xcc) under two different growth conditions: in vivo (Xcc recovered from inoculated B. oleracea leaves) and in vitro (Xcc cultured in rich medium NYG). We chose to begin our

Conclusions

Based on the results obtained in this study, we propose the use of MALDI-Profiling to aid researchers decide and select their samples based on the homogeneity and successful differentiation prior to more complex and costly analyses. Also, the variability among the replicates can be obtained and contribute to better evaluate the experiment. Thus, we believe that MALDI-Profiling offers an inexpensive, rapid and reliable approach for investigating the expression profile, sample differentiation and

Acknowledgements

This work was sponsored by Embrapa, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior- CAPES, Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, and Fundação de Amparo Pesquisa do Distrito Federal FAPDF. We acknowledge the Laboratory of Mass Spectrometry of Embrapa Recursos Genéticos e Biotecnologia for the support in the mass spectrometry analysis.

Author contributions statement

DG Ribeiro; LST Carmo; IR Santos performed protein extraction and sample preparation; LP Silva performed mass spectrometry analysis; OB Oliveira Neto grew the plants and performed inoculations; RF Almeida and JES Pereira prepared the somatic embryogenic material; A Mehta lead the work and prepared the manuscript. All authors reviewed the manuscript.

Declaration of Competing Interest

Authors have no competing interests to declare.

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