MS2 chromatogram alignment for improved protein quantification in large-scale targeted proteomics studies

This poster presents an approach which uses pairwise local alignment of MS/MS-based chromatograms across multiple runs. A dynamic programming-based approach is used to provide non-linear retention time alignment using MS2 chromatogram pairs from distant human plasma runs. It is able to align 98% MS2 peaks within half peak-width compared to 68% by LOESS. Our algorithm is available through an R-package DIAlign