MS-based imaging approaches allow for location-specific identification of chemical components in biological samples, opening up possibilities of much more detailed understanding of biological processes and mechanisms. Data analysis, however, is challenging, mainly because of the sheer size of such datasets. This article presents a novel approach based on self-organizing maps, extending previous work in order to be able to handle the large number of variables present in high-resolution mass spectra. The key idea is to generate prototype images, representing spatial distributions of ions, rather than prototypical mass spectra. This allows for a two-stage approach, first generating typical spatial distributions and associated m/z bins, and later analyzing the interesting bins in more detail using accurate masses. The possibilities and advantages of the new approach are illustrated on an in-house dataset of apple slices

Franceschi, P.; Wehrens, H.R.M.J. (2014). Self-organizing maps: a versatile tool for the automatic analysis of untargeted imaging datasets. PROTEOMICS, 14 (7-8): 853-861. doi: 10.1002/pmic.201300308 handle: http://hdl.handle.net/10449/23590

Self-organizing maps: a versatile tool for the automatic analysis of untargeted imaging datasets

Franceschi, Pietro;Wehrens, Herman Ronald Maria Johan
2014-01-01

Abstract

MS-based imaging approaches allow for location-specific identification of chemical components in biological samples, opening up possibilities of much more detailed understanding of biological processes and mechanisms. Data analysis, however, is challenging, mainly because of the sheer size of such datasets. This article presents a novel approach based on self-organizing maps, extending previous work in order to be able to handle the large number of variables present in high-resolution mass spectra. The key idea is to generate prototype images, representing spatial distributions of ions, rather than prototypical mass spectra. This allows for a two-stage approach, first generating typical spatial distributions and associated m/z bins, and later analyzing the interesting bins in more detail using accurate masses. The possibilities and advantages of the new approach are illustrated on an in-house dataset of apple slices
Apple
Bioinformatics
Metabolites
MS imaging
Self-organizing maps
Imaging
Analisi di dati
Metabolomica
Spettrometria di massa
Settore CHIM/01 - CHIMICA ANALITICA
2014
Franceschi, P.; Wehrens, H.R.M.J. (2014). Self-organizing maps: a versatile tool for the automatic analysis of untargeted imaging datasets. PROTEOMICS, 14 (7-8): 853-861. doi: 10.1002/pmic.201300308 handle: http://hdl.handle.net/10449/23590
File in questo prodotto:
File Dimensione Formato  
Franceschi2014.pdf

solo utenti autorizzati

Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 608.9 kB
Formato Adobe PDF
608.9 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/23590
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 24
  • ???jsp.display-item.citation.isi??? 23
social impact