A Conversation on Data Mining Strategies in LC-MS Untargeted Metabolomics: Pre-Processing and Pre-Treatment Steps

Fidele Tugizimana; Paul A Steenkamp; Lizelle A Piater; Ian A Dubery

doi:10.3390/metabo6040040

A Conversation on Data Mining Strategies in LC-MS Untargeted Metabolomics: Pre-Processing and Pre-Treatment Steps

Metabolites. 2016 Nov 3;6(4):40. doi: 10.3390/metabo6040040.

Authors

Fidele Tugizimana¹, Paul A Steenkamp^{2

3}, Lizelle A Piater⁴, Ian A Dubery⁵

Affiliations

¹ Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa. fideletu@gmail.com.
² Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa. psteenkamp@csir.co.za.
³ Drug Discovery and Development, Biosciences, CSIR, Pretoria 0001, South Africa. psteenkamp@csir.co.za.
⁴ Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa. lpiater@uj.ac.za.
⁵ Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa. idubery@uj.ac.za.

Abstract

Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the "exhaustive" extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter. Data obtained in positive mode generated from a LC-MS-based untargeted metabolomic study (sorghum plants responding dynamically to infection by a fungal pathogen) were used. Raw data were pre-processed with MarkerLynx^TM software (Waters Corporation, Manchester, UK). Here, two parameters were varied: the intensity threshold (50-100 counts) and the mass tolerance (0.005-0.01 Da). After the pre-processing, the datasets were imported into SIMCA (Umetrics, Umea, Sweden) for more data cleaning and statistical modeling. In addition, different scaling (unit variance, Pareto, etc.) and data transformation (log and power) methods were explored. The results showed that the pre-processing parameters (or algorithms) influence the output dataset with regard to the number of defined features. Furthermore, the study demonstrates that the pre-treatment of data prior to statistical modeling affects the subspace approximation outcome: e.g., the amount of variation in X-data that the model can explain and predict. The pre-processing and pre-treatment steps subsequently influence the number of statistically significant extracted/selected features (variables). Thus, as informed by the results, to maximize the value of untargeted metabolomic data, understanding of the data structures and exploration of different algorithms and methods (at different steps of the data analysis pipeline) might be the best trade-off, currently, and possibly an epistemological imperative.

Keywords: chemometrics; data mining; metabolomics; pre-processing; pre-treatment; scaling; transformation.