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MSI Analyst. Software for mass spectrometry imaging experiments.

MSI Analyst

What is MSI Analyst?

MSI Analyst is a new software application for Mass Spectrometric Imaging that enables fast data processing, visualization of MSI experiments and integrates a number of data mining tools that provide new analysis perspectives and a more comprehensive data interpretation.
MSI Analyst works with the formats of major manufacturers and other standards as imzML, includes all the classic tools for processing mass spectrometry data, plus some own developments (for example, eight different types of normalization), and includes graphical tools that provide a new visual experience to the researcher. It also integrates functionalities to semi-automatically identify peaks against a customizable database of molecules.


  • Fast and comprehensive processing. Import, filter, align and normalize to get the data ready in just a couple of minutes.
  • Intuitive and powerful visualization, through new visual components and tools thanks to the XNA technology.
  • Automation of the extraction of knowledge. Integrated data mining tools automate the detection of differential regions and the identification of compounds.
  • Easy management of experiments, processes and compounds.
  • Automated reports. Get a comprehensive report on your results with just one click.

Key features

Data pre-treatment

  • Filtering by mass.
  • Filter by intensity (signal to Noise Ratio / Percentage of the Maximum / Polynomic Fit Threshold).
  • Peak discarding.
  • Binning methods: Standard Binning / Centre of Mass Binning.
  • Smoothing: Savitzky-Golay method.
  • Baseline correction: Stretches / Polynomial fitting.
  • Peak selection: Naïve / Simple Peak Finding.
  • Life pre-visualization of the effects of the filters over the spectra data to make easy the decision taking.

Alignment and Calibration

  • Alignment: Block Alignment / Xiong Method.
  • Block calibration.


  • 8 normalization methods: Total Ion Current / P-norm / Mean / Median / Noise Level / Maximum / TIC with range exclusion / Normalization against selected peak.

Data Management

  • Intuitive Experiments management: List / Filtering / Browse / Tree-view of Processes associated to an experiment.
  • Compound Database: Search / Import From File or Add Manually / Edit / Group.
  • Automated and comprehensive reports.

Data Visualization

  • Peak distributions: display and scrutinize two dimensional molecule distribution in tissues.
  • Get average spectrums of the whole experiment or a certain region of interest.
  • Identify compounds.
  • Visualize "mass videos" made of shots of average spectrum peaks' distributions in the tissue.
  • Select from more than 20 colour gradients.
  • Fix colour-intensity ranges.
  • Zoom images and spectra.

Compound database

  • Exportation to file of images and spectra.
  • Import, search and manage compounds.
  • The updateable pre-loaded database includes more than 33.000 lipids, although it accepts any kind of molecule.
  • Peaks identification. Find all the ionized compound candidates for a given peak / Get a list of candidates for all the peaks on the average spectrum.

Statistical Analysis: Principal Component Analysis

  • Three algorithms: Classical PCA / Iterative PCA / Landmark Isomap.
  • Automatically finds differentiated regions of the tissue according to their composition.
  • Visualize the distribution of the individual components.
  • Display the Principal Components coefficients graph.

Statistical Analysis: Clustering

  • Two algorithms: K-MEANS / Partitional Hierarchical Clustering.
  • Finds differentiated regions and assigns each tissue point to one or another.
  • Show each cluster's average spectrum.
  • Biomarker identification: Get main peaks involved in a cluster.


    MSI Analyst was developed in close collaboration with the group GEsEM of The University of the Basque Country, and used in the following work:
  • R. Fernández, S. Lage, B. Abad, G. Barceló, S. Terés, D. H. López, F Guardiola, M. L. Martín, P. V. Escribá and J. A. Fernández. Analysis of the lipidome of xenografts using MALDI-IMS and UHPLC-ESI-QTOF, J. Am. Soc. Mass Spectrom. 2014, Accepted for publication
It was also reviewed in the following publication:

Noray Bioinformatics, S.L.U.
Parque Tecnológico de Bizkaia
Edif. 801A, 2º
48160 - Derio - Spain
+34 94 403 6998