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adductomicsR: A package for detection and quantification of protein adducts from mass spectra of tryptic digests

By Josie Hayes, William M. B. Edmands, Yukiko Yano, Hasmik Grigoryan, Courtney Schiffman, Sandrine Dudoit, Stephen M. Rappaport

Posted 06 Nov 2018
bioRxiv DOI: 10.1101/463331

Summary: Liquid chromatography-high resolution mass spectrometry (LC-HRMS) has been used to establish a method, referred to as adductomics, for characterisation of putative protein adducts at selected loci in human serum albumin (HSA). Applications of this method have been limited by the lack of software for untargeted analysis of modified peptides in protein digests. Here we present adductomicsR, an open-source R package for processing LC-HRMS data from analysis of adducted HSA peptides. The software interrogates mass spectra to correct for retention-time drift, and to discover and quantify putative adducts along with those for a housekeeping peptide and internal standard. Availability and implementation: adductomicsR is written in R and publicly available at https://github.com/JosieLHayes/adductomicsR, which includes a vignette with example data. Supplementary information: mzXML files for the vignette and test dataset are available in an associated data package adductData (https://github.com/JosieLHayes/adductData).

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