EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data.

Wijetunge CD, Saeed I, Boughton BA, Spraggins JM, Caprioli RM, Bacic A, Roessner U, Halgamuge SK
Bioinformatics. 2015 31 (19): 3198-206

PMID: 26063840 · DOI:10.1093/bioinformatics/btv356

MOTIVATION - Matrix Assisted Laser Desorption Ionization-Imaging Mass Spectrometry (MALDI-IMS) in 'omics' data acquisition generates detailed information about the spatial distribution of molecules in a given biological sample. Various data processing methods have been developed for exploring the resultant high volume data. However, most of these methods process data in the spectral domain and do not make the most of the important spatial information available through this technology. Therefore, we propose a novel streamlined data analysis pipeline specifically developed for MALDI-IMS data utilizing significant spatial information for identifying hidden significant molecular distribution patterns in these complex datasets.

METHODS - The proposed unsupervised algorithm uses Sliding Window Normalization (SWN) and a new spatial distribution based peak picking method developed based on Gray level Co-Occurrence (GCO) matrices followed by clustering of biomolecules. We also use gist descriptors and an improved version of GCO matrices to extract features from molecular images and minimum medoid distance to automatically estimate the number of possible groups.

RESULTS - We evaluated our algorithm using a new MALDI-IMS metabolomics dataset of a plant (Eucalypt) leaf. The algorithm revealed hidden significant molecular distribution patterns in the dataset, which the current Component Analysis and Segmentation Map based approaches failed to extract. We further demonstrate the performance of our peak picking method over other traditional approaches by using a publicly available MALDI-IMS proteomics dataset of a rat brain. Although SWN did not show any significant improvement as compared with using no normalization, the visual assessment showed an improvement as compared to using the median normalization.

AVAILABILITY AND IMPLEMENTATION - The source code and sample data are freely available at http://exims.sourceforge.net/.

CONTACT - awgcdw@student.unimelb.edu.au or chalini_w@live.com

SUPPLEMENTARY INFORMATION - Supplementary data are available at Bioinformatics online.

© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

MeSH Terms (9)

Algorithms Animals Brain Eucalyptus Metabolomics Plant Leaves Proteomics Rats Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

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