DIAlignR 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.

Travis build status


For documentation please see our vignette.

Developing C++ code

cd DIAlignR
mkdir build && cd build
cmake -B. -H.. 
make clean && make && make test
make runTest3
cd ..

Documenting C++ code

sudo apt install doxygen doxygen-gui 
sudo apt install graphviz
cd DIAlignR
cd src
doxygen doc/Doxyfile


If you use the provided algorithms or the package, please cite our paper:

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: Epub 2019 Jan 31.

CNPN 2018 Poster doi: HUPO 2018 Poster doi:

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DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.