Software tools of the Computis European project to process mass spectrometry images

Marie France Robbe, Jean Pierre Both, Brendan Prideaux, Ivo Klinkert, Vincent Picaudd, Thorsten Schramm, Alfons Hester, Victor Guevara, Markus Stoeckli, Andreas Roempp, Ron Heeren, Bernhard Spengler, Olivier Gala, Serge Haana

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Among the needs usually expressed by teams using mass spectrometry imaging, one that often arises is that for user-friendly software able to manage huge data volumes quickly and to provide efficient assistance for the interpretation of data. To answer this need, the Computis European project developed several complementary software tools to process mass spectrometry imaging data. Data Cube Explorer provides a simple spatial and spectral exploration for matrix-assisted laser desorption/ionisation-time of flight (MALDI-ToF) and time of flight-secondary-ion mass spectrometry (ToF-SIMS) data. SpectViewer offers visualisation functions, assistance to the interpretation of data, classification functionalities, peak list extraction to interrogate biological database and image overlay, and it can process data issued from MALDI-ToF, ToF-SIMS and desorption electrospray ionisation (DESI) equipment. EasyReg2D is able to register two images, in American Standard Code for Information Interchange (ASCII) format, issued from different technologies. The collaboration between the teams was hampered by the multiplicity of equipment and data formats, so the project also developed a common data format (imzML) to facilitate the exchange of experimental data and their interpretation by the different software tools. The BioMap platform for visualisation and exploration of MALDI-ToF and DESI images was adapted to parse imzML files, enabling its access to all project partners, more globally, to a larger community of users. Considering the huge advantages brought by the imzML standard format, a specific editor (vBrowser) for imzML files and converters from proprietary formats to imzML were developed to enable the use of the imzML format by a broad scientific community. This initiative paves the way toward the development of a large panel of software tools able to process mass spectrometry imaging datasets in the future.

Original languageEnglish (US)
Pages (from-to)351-360
Number of pages10
JournalEuropean Journal of Mass Spectrometry
Volume20
Issue number5
DOIs
StatePublished - Oct 7 2014
Externally publishedYes

Fingerprint

software development tools
format
Mass spectrometry
Desorption
mass spectroscopy
desorption
Ionization
ionization
Electrospray ionization
Secondary ion mass spectrometry
Imaging techniques
Lasers
files
Visualization
secondary ion mass spectrometry
matrices
lasers
Interchanges
flight time
registers

Keywords

  • Clustering
  • Image processing
  • Image registration
  • Imaging mass spectrometry
  • Standard format
  • Visualisation

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics
  • Spectroscopy

Cite this

Software tools of the Computis European project to process mass spectrometry images. / Robbe, Marie France; Both, Jean Pierre; Prideaux, Brendan; Klinkert, Ivo; Picaudd, Vincent; Schramm, Thorsten; Hester, Alfons; Guevara, Victor; Stoeckli, Markus; Roempp, Andreas; Heeren, Ron; Spengler, Bernhard; Gala, Olivier; Haana, Serge.

In: European Journal of Mass Spectrometry, Vol. 20, No. 5, 07.10.2014, p. 351-360.

Research output: Contribution to journalArticle

Robbe, MF, Both, JP, Prideaux, B, Klinkert, I, Picaudd, V, Schramm, T, Hester, A, Guevara, V, Stoeckli, M, Roempp, A, Heeren, R, Spengler, B, Gala, O & Haana, S 2014, 'Software tools of the Computis European project to process mass spectrometry images', European Journal of Mass Spectrometry, vol. 20, no. 5, pp. 351-360. https://doi.org/10.1255/ejms.1293
Robbe, Marie France ; Both, Jean Pierre ; Prideaux, Brendan ; Klinkert, Ivo ; Picaudd, Vincent ; Schramm, Thorsten ; Hester, Alfons ; Guevara, Victor ; Stoeckli, Markus ; Roempp, Andreas ; Heeren, Ron ; Spengler, Bernhard ; Gala, Olivier ; Haana, Serge. / Software tools of the Computis European project to process mass spectrometry images. In: European Journal of Mass Spectrometry. 2014 ; Vol. 20, No. 5. pp. 351-360.
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