Binning	A range (e.g., m/z or Rt shift values) is divided into a series of equally long intervals (bins).
Dataset	A list of LC-HRMS datafiles belonging to one analytical batch, originating from the same experiment.
EIC	Extracted ion chromatogram. An EIC represents the abundance/intensity of a certain m/z value in each mass spectrum of a chromatogram. The mass spectra are sorted according to their acquisition time relative to injecting the sample into the HPLC instrument. Usually a small deviation from the selected m/z value (± ppm; depending on the used HRMS instrument) is allowed to account for minor scan-to-scan m/z inconsistencies observed during acquisition of a chromatogram.
Feature	A feature represents a particular metabolite ion of interest. It is characterized by its m/z value (experimental and theoretical) and retention time (as calculated by the used peak-picking algorithm). Features are usually the result of an untargeted metabolomics data processing approach and typically comprise multiple chromatographic peaks, one per LC-HRMS chromatogram.
Feature group	All features originating from the same chemical substance and hence sharing the same Rt and peak shape.
F-measure	Harmonic mean of precision and recall.
Fn	False negatives. Features that were not matched.
Fp	False positives. If a matched feature does not meet the criteria to be considered as Tp, it is an Fp.
LC-HRMS	Liquid chromatography coupled to high resolution mass spectrometry.
m/z	Mass-to-charge ratio.
Peak/Chromatographic peak	A chromatographic peak representing a particular feature in a chromatogram. Other than a feature, a peak has a defined m/z value, a retention time (as defined by the used peak-picking algorithm) as well as a peak area. Peaks are detected by the means of a peak-picking algorithm.
Peak apex	The time at which the most abundant signal of a respective chromatographic peak is detected after injection of the sample into the HPLC instrument.
Peak center	The time at which a chromatographic peak has its center of gravity. (Time) measurement is started with injecting the sample into the HPLC instrument.
Precision	Percentage of matched reference features that were correctly matched. Calculation: Number of Tp divided by the number of Tp plus Fp.
Recall	Percentage of all reference features that were correctly matched. Calculation: Number of Tp divided by the number of all reference features.
Reference dataset	A single or multiple LC-HRMS datafiles, which are used to generate the reference feature list.
Reference feature list	List of features to which target datasets are matched.
Rt	Retention time.
Rt shift function	A function that holds the calculated retention time shift between a target chromatogram relative to the reference feature list. It is used to map the retention times of detected chromatographic peaks in the target chromatogram to the retention time of the features in the reference list.
Search frame	Signals of a chromatogram (single datafile) that fall within a certain Rt and m/z tolerance window around a reference feature. These values have to be slightly larger than the maximum expected shift. (e.g., 1.5 min Rt shift and 10 parts per million (ppm) m/z shift for a typical LC-HRMS chromatogram).
Rt shift array	An array containing the Rt shift of all peaks detected within a search frame relative to the retention time of the respective reference feature. First, a search frame is discretized into smaller bins (number of bins is set by the user of MetMatch) each representing a certain Rt offset relative to the retention time of the respective reference feature. Then, those Rt bins for which chromatographic peaks of the respective reference feature were detected in the target chromatogram, are assigned weight values greater than zero (either automatically or user-guided). Any Rt offset bin for which no chromatographic peak was detected, is assigned zero value and thus do not contribute to the Rt shift detection algorithm. The number of entries in each Rt shift array is set by the user during the iterative Rt alignment step. Each entry in the Rt shift array corresponds to a certain Rt deviation between the retention times of the reference features and their corresponding chromatographic peaks in the target chromatograms.
Rt shift matrix	The individual Rt shift arrays of all reference feature groups are concatenated column-wise and sorted by the retention time of their reference feature group. Each column represents a feature group, while rows represent discretized Rt shift values.
Target dataset	A list of LC-HRMS datafiles to be matched to a reference feature list.
Tp	True positives. Matched features are considered Tp if their m/z deviation is ≤5 ppm and their Rt deviation is ≤8.4 s (manually validated threshold value for the distinction of Tp and Fp in this datafile) relative to the reference feature after shift correction. The formation of different ion species is taken into account when comparing the m/z.