mineXpert2 is a mass spectrometric data visualization and exploration software.

mineXpert2 comprises the following main features

Load any kind of mass spectrometry data files

mineXpert2 can load mzML, mzXML, MGF, Bruker timsTOF (natively) formats. Further, it recognizes automagically the (x y) and BafAscii (Bruker) text formats. mineXpert2 can load a mass spectrum directly from the clipboard.

mineXpert2 overview

File loading is fully parallelized so that it is possible to read from disk any number of files simulateously. The file loading process is automatically followed by the computation of the total ion current chromatogram (TIC chromatogram) that is shown right after MS data loading. That TIC chromatogram would typically be used as the starting point for a data visualization and exploration session.

For most file formats, when the file is too large to fit in the RAM of the computer (memory), the user is provided the possibility to open the file in streamed mode. Although the exploration might prove a bit slower, at least it can be performed!

Unlimited combination of mass spectrometric data integrations

A typical session of mass data analysis and exploration begins with the visualization of the TIC chromatogram. From there, one may inquire about the analytes eluted in a particular region of the chromatogram. To do this, integration of the region of interest from the TIC chromatogram to a mass spectrum could be performed, for example. Visualizing the mass spectrum could give an idea of whether certain analytes exhibit different ion mobilities. One might then integrate the mass spectrometry peak at the desired m/z value to a mobility spectrum. This could reveal that the analyte exhibits a complex mobility profile. Then, one could question the retention time of ions under different mobility times. For this, one could separately integrate the different ion mobility peaks to an extracted ion current chromatogram.

This process is illustrated in the image below, with the same integration sequence as described above. The full TIC chromatogram is integrated to the mass spectrum (above) and the zoomed-in main mass peak is then integrated to an ion mobility spectrum. The ion mobility spectrum shows that during the acquisition, the analyte at the initial m/z ratio has four main ion mobility modes. When integrating separately each peak of the ion mobility spectrum to an extracted ion current chromatogram (XIC), we can see that each has a different retention time.

mineXpert2 overview

The dataset used for the illustration above was courtesy of Valérie Gabelica and corresponds to a work entitled Optimizing Native Ion Mobility Q-TOF in Helium and Nitrogen for Very Fragile Noncovalent Structures> published in JASMS with* DOI: 10.1007/s13361-018-2029-4.

In the figure above, the TIC chromatogram computed at file data loading time is the one at the top of all the chromatograms (left window). Integrating the whole retention time range to a mass spectrum did produce the mass spectrum (full m/z range above and zoomed-in peak below) in the window top-right. The ion mobility analysis of the ubiquitin oligopeptide was performed by modifying the instrument parameters over the mass spectrometric acquisition. This is shown in the ion mobility spectrum (bottom-right window) where the single mass peak (lower trace top-right window) was integrated to an ion mobility spectrum. There are five pretty well resolved ion mobilities for this single mass peak. The back-integration of each mobility peak to a XIC chromatogram (all the chromatograms in the left window less the first one), one can see when, in the acquisition, the instrument parameters were changed to reveal/trigger different ion mobilities for the same ion (as identified with a m/z value).

Powerful and flexible visualization widgets

Data visualization has been the primary concern throughout the development of the mineXpert2 software. The goal was to enable navigation through all depths of the data, in MS1, but also for any level of fragmentation (not only MS/MS, but MSn as well). Two types of visualization are available:

  • Trace mode visualization, such as mass spectrum or XIC chromatogram, or even ion mobility spectrum;

  • Color map mode visualization, such as m/z vs retention time or m/z vs ion mobility, or retention time vs ion mobility. These maps are illustrated below.

mineXpert2 overview

A clear organization of the products of data visualization and exploration.

For each dataset loaded from a file, a color is assigned, which is then used for all traces, color maps, and related products associated with that dataset.

TIC and XIC chromatograms are displayed in a dedicated window. The same applies to mass spectra, mobility spectra, and various maps.

This methodology allows for displaying different windows on the screen to manage visualization in an intuitive manner.

Each visualization unit contains the same widgets allowing for tasks that are common across all types of visualization. The figure below shows these visualization units (composite widgets) for some of the visualization types (from top to bottom: TIC or XIC chromatogram, mass spectrum, drift spectrum, ion mobility vs m/z map).

mineXpert2 overview

One can recognize a button bar on the left and another on the right. The left bar controls how the data is displayed in the composite widget (adding a new trace, for example). The right bar controls the destination of the next integration of mass spectrometry data. For example, the MZ icon indicates integration towards a mass spectrum, while the DT icon indicates integration towards a mobility spectrum (DT: drift time).

Tabular visualization of mass spectrometry data

It is possible to display the data from a dataset in a spreadsheet-style table view. The data can be filtered according to various criteria that can be combined to extract the desired data element (see figure below).

mineXpert2 overview

The “Filtering options” widget allows for data filtering. Once only the relevant data is retained, the buttons in the bottom row trigger the corresponding integration only with the data currently selected in the table view.

An application tailored for comparing data

Particular care has been taken to allow for easy comparison of data. It is possible to duplicate one trace onto another with a simple mouse click to compare them by overlaying. It is possible to increment a spectrum by adding another spectrum. The same goes for subtracting one spectrum from another, which is useful for eliminating background noise.

Exporting visualized data to different formats

It is possible to export any trace or map as text to a file. Additionally, it is possible to export a graphical representation of a given widget to the clipboard or to a file for later use in a publication. Exporting to the SVG format is particularly suitable for this purpose.