Software Tools of the Computis European Project to Process Mass Spectrometry Images

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 and, 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.

Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview

“…Sophisticated software tools to process MS images were also developed by international consortia aiming to develop and strengthen technologies and methods for MSI. One such initiative, the COMPUTIS consortia consisting of academic and industrial institutes have launched the DataCube Explorer, SpectViewer, and the EasyReg2D tools [61]. These programs and tools are user-friendly and permit to manage huge data sets quickly and to provide efficient assistance for the visualization and interpretation of data.…”

Comparison of Two Freely Available Software Packages for Mass Spectrometry Imaging Data Analysis Using Brains from Morphine Addicted Rats

“…The most recognized ones belong to that group are: BioMap (Novartis/IDL) and Datacube (FOM-Amolf). 7,8 The scientists who developed their own MS-imaging ion sources, or who do not have access to the original software, have to rely on the freely available programs. In this work, we compared the capabilities of the most popular software packages, BioMap and Datacube, of those freely available.…”

MALDI mass spectrometric imaging meets “omics”: recent advances in the fruitful marriage

“…enzymatic digestion, 25,26 derivatization, 27 transfer to functionalized surfaces), 28 and instrumentation for the application of the matrix. 50,[52][53][54][55][56][57][58] Finally, in drug imaging, 59, 60 besides ion traps (FT-ICR and Orbitrap), triple quadropole analyser is additionally in favour, due to its selected reaction monitoring capabilities. 34 Hence, the optimization of all these parameters based on the type of sample, ranking from human, animal, plant, food tissue, cells, cosmetics, to polymeric materials, is essential for the outcome of the MALDI MSI experiment.…”