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Assign MALDI MS2s to features


Feature list methods → Processing → Assign MALDI MS2s to features

This module allows to pair MS2 scans with features. It uses the spot information stored in the MS1 feature list and the MS2 spectra, the precursor m/z, and the ion mobility windows to pair the MS2s. Be careful when processing multiple imaging datasets with different geometries (multiple flexImaging run files). Among different geometries, multiple spots can have the same coordinate, as they are just stored as a location. This can lead to wrong assignments for abundant species. Make sure to only select the correct MS2 files, e.g., with a more specific name pattern.


MS2 scan pairing dialog

Feature lists

Select the feature lists to pair the MS2s to

Raw data files

The raw data files containing the MS2 spectra. By default, "File name pattern" with the pattern "*_MSMS*" is selected, due to the naming of the MS2 files. More specific patterns, such as " *RUN1*_MSMS*" can be used.

MS1 to MS2 precursor tolerance (m/z)

Describes the tolerance between the precursor ion in a MS1 scan and the precursor m/z assigned to the MS2 scan.

Combine MS/MS spectra (TIMS)

If checked, all MS/MS spectra assigned to a feature will be merged into a single spectrum. Individual spectra are retained. Usually this is not required, because MS2s can be merged during library matching.

Lock to feature mobility range

If checked, only mobility scans from the mobility range of the feature will be merged.

⚠ This is usually not needed. However, if isomers/isobars elute at the same retention time and are close in mobility, the MS/MS window might be larger than the peak in mobility dimension and thus cause chimeric MS/MS spectra.

Minimum merged intensity

If an ion mobility spectrometry (IMS) feature is processed, this parameter can be used to filter low abundant peaks in the MS2 spectrum, since multiple MS/MS mobility scans need to be merged together.

Steffen Heuckeroth

Last update: November 13, 2023 11:26:25