adductomicsR: A package for detection and quantification of protein adducts from mass spectra of tryptic digests
| Autor: | Josie Hayes, Sandrine Dudoit, Courtney Schiffman, Stephen M. Rappaport, William M. B. Edmands, Hasmik Grigoryan, Yukiko Yano |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
chemistry.chemical_classification
010504 meteorology & atmospheric sciences Putative protein Protein adducts Peptide Computational biology 010501 environmental sciences Human serum albumin 01 natural sciences R package Adductomics chemistry Mass spectrum medicine Mass spectrometry data format 0105 earth and related environmental sciences medicine.drug |
| DOI: | 10.1101/463331 |
| Popis: | SummaryLiquid 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 implementationadductomicsR is written in R and publicly available at https://github.com/JosieLHayes/adductomicsR, which includes a vignette with example data.Supplementary informationmzXML files for the vignette and test dataset are available in an associated data package adductData (https://github.com/JosieLHayes/adductData).Contactjosie.hayes@berkeley.eduIssue SectionAPPLICATIONS NOTE |
| Databáze: | OpenAIRE |
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