Biology subjects

Rost, H.

Publications and source records attributed to Rost, H..

2 recordsLinked to original sources

bioRxiv2020

Automated Workflow For Peptide-level Quantitation From DIA/ SWATH-MS Data

Data Independent Acquisition (DIA) is a powerful method to acquire spectra from all ionized precursors of a sample. Considering the complexity of the highly multiplexed spectral data, sophisticated workflows have been developed to obtain peptides quantification. Here we describe an open-source and easy-to-use workflow to obtain a quantitative matrix from multiple DIA runs. This workflow requires as prior information an "assay library", which contains the MS coordinates of peptides. It consists of OpenSWATH, pyProphet and DIAlignR software. For the ease of installation and to isolate operating system related dependency, docker-based containerization is utilized in this workflow.

bioinformatics↗

bioRxiv2020

DrawAlignR: An interactive tool for across run chromatogram alignment visualization

Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.

bioinformatics↗