DIAlignR

Overview

DIAlignR [1] is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.

Contact and Support

We provide support for DIAlignR on the GitHub repository.

You can contact the author Shubham Gupta.

Tutorial

DIAlignR provides a vignette that explains the installation and usage of the package. You can also find more full extensive examples of the data analysis from [1] and [2] on the GitHub wiki.

References

[1] (1,2)

Gupta S, Ahadi S, Zhou W, Röst H. “DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.” Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: https://doi.org/10.1074/mcp.TIR118.001132 Epub 2019 Jan 3

[2]

Gupta, S., Sing, J.C. & Röst, H.L. Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment. Commun Biol 6, 1101 (2023). https://doi.org/10.1038/s42003-023-05437-2