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Ion mobility raw data overview (LC-IMS-MS)


Visualization → Ion mobility raw data overview

The "Ion mobility raw data visualization" module allow a comprehensive navigation of the complex LC-IM-MS raw data. The screenshot belows shows an example of LC-IM-MS data acquired with a Bruker timsTOF instrument:


The main window consists of 5 panels and a set of displaying parameters. All the panels are interconnected, which means that moving the cursor in one panel, automatically updates the others. Cursors are displayed as light-blue solid lines in the panels.

Summed frame spectrum panel [1]

The MS spectrum corresponding to each frame is shown in this panel. The displayed MS spectrum is the sum of all the mobility scans acquired over that frame (see Ion mobility spectrometry terminology).

BPC panel [2]

In this panel, the base peak chromatogram is displayed. Each data point corresponds to an individual frame. Moving the cursor frame-by-frame automatically updateds the 'frame heatmap' and 'summed frame spectrum' panels. Moving the cursor frame-by-frame automatically updateds the 'summed frame spectrum' panels as changing data point in regular LC-MS data would display a different MS scan. Since each frame is made of several mobily scans, the 'mobilogram chart' and 'frame heatmap' panels automatically updates too. Note. It is currently not possible to display the TIC chromatogram)

Mobility scan [3]

Mobilogram chart [4]

Frame heatmap [5]

Ion trace chart [6]

Displaying parameters [6]

Mobility scan noise level: This parameter controls the signals shown in the XXX panels (panel n°X). For example, a noise level of 5.0E1 will show only the signals above this value (see below)

Frame noise level: This parameter sets a threshold for the signals shown in the "Summed frame spectrum panel" (panel n°X). Signals from MS spectra acquired over the same frame are summed and shown

m/z tolerance

Scan selection

Retention time width

Mobilogram bin width (abs)

EIC/mobilogram ranges

Steffen Heuckeroth, omokshyna, tdamiani

Last update: November 24, 2022 21:13:07