MALDI spot feature detection¶
Description¶
Feature list methods → Feature detection → MALDI spot feature detection
This module detects features in MALDI dried-droplet spots directly from native timsTOF fleX
imaging data (.d folder). It only works with imaging raw data files acquired with this instrument.
For each MALDI spot found in the data, a separate feature list is produced. Every signal in the spot's frame spectrum that exceeds the Minimum intensity threshold is recorded as an individual feature row. This gives one feature per detected m/z per spot, allowing downstream modules (spectral library matching, formula prediction, etc.) to be applied on a per-spot basis.
If the raw data were acquired with ion mobility (timsTOF fleX TIMS mode), the detected features are automatically expanded into the mobility dimension by running the IMS Expander internally for each spot feature list using the same m/z tolerance.
Warning
Mass detection must be run before this module. Features are detected from the processed mass list, not from the raw spectral data.
Parameters¶
Raw data files¶
The raw data files to process.
m/z tolerance¶
m/z tolerance used to group data points during IMS expansion (for timsTOF fleX data with TIMS). Default: ±0.005 Da or ±15 ppm (whichever is larger).
Minimum intensity¶
Minimum intensity a signal must reach in the frame spectrum to be detected as a feature. Data points below this threshold are not processed. Default: 5,000.
Spot sample names (Optional)¶
Path to a semicolon-delimited CSV file (.csv) that maps MALDI spot identifiers to human-readable
sample names. The file must contain at least two columns with headers spot and name (
case-insensitive). Additional columns are ignored.
Each spot's feature list is named <name> - <spotId>. If no mapping file is provided, or if a spot
identifier is not found in the file, the raw data file name is used as the prefix instead.
Example CSV content:
spot;name;treatment
A1;Control_1;blank
B2;Sample_A;compound_X
Output¶
One feature list is created per MALDI spot in the data. The feature list name follows the pattern
<sampleName> - <spotId>, where <sampleName> comes from the spot name mapping file (or the raw
data file name as fallback) and <spotId> is the spot identifier recorded in the raw data.
For IMS data, each feature list entry contains a mobilogram (intensity vs. mobility profile) in addition to the MS1 signal.