ncGTW

ncGTW detects misaligned feature groups from XCMS and realigns LC-MS profiles using compound-specific graphical time warping with neighbor-wise constraints.

Key Features:

• Misalignment Detection: ncGTW identifies misaligned feature groups produced by XCMS that would otherwise be discarded or remain uncorrected.
• Compound-Specific Warping: ncGTW uses individualized warping functions for different compounds rather than assuming a single time-warping function per sample.
• Neighbor-wise Constraints: ncGTW assigns constraint edges on warping functions of neighboring samples to leverage expected retention time drift structures across run order.
• XCMS Integration: ncGTW operates as a plug-in to the XCMS package, allowing users to selectively realign detected misaligned feature groups.
• Reference-Free Alignment: ncGTW performs alignment without requiring an external reference sample.

Scientific Applications:

• Metabolomics LC-MS Data Analysis: ncGTW corrects retention time drift in large-scale metabolomics datasets where misalignment is inevitable.
• Proteomics LC-MS Data Analysis: ncGTW addresses retention time variation in proteomics experiments analyzed by liquid chromatography-mass spectrometry.
• Large-Scale Experiment Quality Control: ncGTW validates alignment performance using internal quality control samples and realistic synthetic data.

Methodology:

ncGTW applies neighbor-wise compound-specific Graphical Time Warping with constraint edges on warping functions of neighboring samples to model expected retention time drift structures and compound-specific warping functions.