DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics

Area of Science:

• Proteomics
• Mass Spectrometry
• Bioinformatics

Background:

• Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH-MS) is a high-throughput proteomics technique.
• Quantification consistency in large-scale SWATH-MS studies is challenged by sample heterogeneity and technical variability.
• Retention time (RT) reproducibility is critical for SWATH-MS data analysis but is often affected by experimental factors.

Purpose of the Study:

• To develop a novel algorithm for robust retention time (RT) alignment of SWATH-MS data.
• To improve the accuracy and consistency of analyte quantification in large-scale proteomics studies.
• To address challenges posed by sample heterogeneity and technical variability in SWATH-MS data analysis.

Main Methods:

• A new algorithm, DIAlignR, was developed for RT alignment using direct alignment of raw MS2 chromatograms.
• The algorithm employs a hybrid dynamic programming approach, allowing for non-chronological and elution-order-swapped peak alignment.
• RT mapping is performed within a window around a coarse global fit, enhancing robustness against noise.

Main Results:

• DIAlignR outperformed state-of-the-art methods on a manually validated dataset.
• On real-world clinical data, DIAlignR mapped 98% of peaks compared to 67% for global alignment methods.
• The algorithm reduced alignment error up to 30-fold for distant runs and demonstrated robustness.

Conclusions:

• DIAlignR provides a robust and accurate solution for retention time alignment in SWATH-MS data.
• The developed algorithm significantly enhances quantification consistency for large-scale and heterogeneous proteomics studies.
• DIAlignR offers improved performance over existing methods, facilitating more reliable proteomic analyses.