OBI-Warp

OBI-Warp performs retention-time alignment of ESI-LC-MS and LC-MS/MS chromatographic profiles using an ordered bijective interpolated warping extension of dynamic time warping to enable accurate peptide and protein comparisons across experiments.

Key Features:

• Ordered Bijective Interpolated Warping: Extends dynamic time warping (DTW) to produce an ordered, one-to-one correspondence between aligned datasets for proteomic comparisons.
• Smooth Warping Function: Applies piecewise cubic Hermite interpolation to DTW outputs to generate smooth warping functions for chromatographic alignment.
• Optimization with High-Confidence Standards: Optimizes alignment parameters using high-confidence, overlapping tandem mass spectra as standards across ESI-LC-MS datasets.
• Performance Metrics: Evaluates spectra similarity using Pearson's correlation coefficient and reports superiority over covariance, dot product, and Euclidean distance for alignment assessment.
• Gap Penalization: Incorporates gap penalization during alignment to improve retention-time matching across different experimental conditions.

Scientific Applications:

• Proteomics comparative analysis: Aligns MS signals from multiple LC-MS/MS and ESI-LC-MS experiments to overcome chromatographic retention time variability and improve peptide and protein identification and quantitation.

Methodology:

Selection of diverse ESI-LC-MS datasets, computation of dynamic time warping (DTW) to produce an ordered bijective function, application of piecewise cubic Hermite interpolation to obtain smooth warping functions, optimization of alignment parameters using high-confidence overlapping tandem mass spectra, and incorporation of gap penalization during alignment.