GC-EI Feature Alignment¶
Description¶
Feature list methods → Alignment → GC aligner
This module aligns GC/EI-MS feature lists by grouping deconvoluted features based on their retention times and spectral similarities to ensure accurate alignment of features across different samples.
Tip
GC aligner requires mass spectra to be constructed prior to the alignment (using GC-EI spectral deconvolution).
A typical workflow can be constructed with the mzwizard by selecting GC-EI-MS. See this pagefor a more detailed description of the workflow.
Parameters¶
Feature lists¶
Select the feature lists to be aligned.
m/z Tolerance (scan-to-scan)¶
Tolerance for m/z values used for spectral similarity matching.
Retention time tolerance¶
Maximum allowed difference between two retention time values for them to be considered for alignment.
Weight for RT¶
Score for perfectly matching RT values. The RT delta is divided by the RT tolerance and scaled 0-1. The weight then multiplies this score so that higher RT delta gives a penalty. The RT weight shifts the focus on RT or spectral similarity.
Similarity¶
Algorithm to calculate spectral similarity between samples. Pseudo spectra from GC-EI spectral deconvolution will be compared. Usually uses the Composite cosine identity which is similar to the algorithm in NIST search for GC-EI data.
Feature list name¶
Name for the aligned feature list.
Original feature list¶
Either keep or remove the original feature lists.
Tip
The alignment is performed independtly of the representative feature. Only spectral similarity and retention time are taken into account. The final representative feature will be determined as during the alignment.