PtH2O2lipids

Repository for the R data package PtH2O2lipids. PtH2O2lipids contains processed, positive ionization mode HPLC-ESI-MS lipid data from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. If citing this package, please also cite this manuscript. Currently, the files must be compiled into a package on the user's machine using devtools. Installation directions are below.

Package description

Upon executing library(PtH2O2lipids), a list object ptH2O2lipids is loaded into the user's environment. ptH2O2lipids consists of the positive ionization mode data in several states:

1. ptH2O2lipids$xsAnnotate: An 80 MB CAMERA "xsAnnotate" object containing annotated, positive ionization mode HPLC-ESI-MS lipid data that have been assigned to 5,080 pseudospectra. Includes annotation of possible isotope peaks from findIsotopes. The xcms xcmsSet from which the xsAnnotate object was created (64.5 MB) can be accessed at PtH2O2lipids$xsAnnotate@xcmsSet. The xcmsSet was created from 16 positive mode mzXML files containing centroided data from an Exactive Orbitrap mass spectrometer in the Van Mooy Lab at WHOI. Conversion of the original Thermo .raw files to .mzXML was accomplished using an implentation of the msconvert command-line tool in Exactive_full_scan_process_ms1+.r. The PtH2O2 xcmsSet and xsAnnotate objects were created from the source .mzXML files (see link to download below) using the xcms and CAMERA settings in the script prepOrbidata.R. Both Exactive_full_scan_process_ms1+.r and prepOrbidata.R can be found in the Van Mooy Lab Lipidomics Toolbox.

2. ptH2O2lipids$LOBSet: A 1.2 MB LOBSTAHS "LOBSet" object containing screened peak data (accessed via peakdata(ptH2O2lipids$LOBSet)) to which compound identifications have been made from the default LOBSTAHS positive mode database. The object also includes in the slots iso_C3r, iso_C3f, and iso_C3c the various possible isomers identified for each compound. ptH2O2lipids$LOBSet was created using:

doLOBscreen(xsAnnotate, polarity = "positive", database = NULL,
            remove.iso = TRUE, rt.restrict =  TRUE, rt.windows = NULL,
            exclude.oddFA = TRUE, match.ppm = 2.5)

Arguments of NULL for database and rt.windows cause the function to use the package default database and retention time windows. Generation of the database was accomplished using the LOBSTAHS function generateLOBdbase(). Methods used to create the databases and retention time windows are described in Collins, J.R., B.R. Edwards, H.F. Fredricks, and B.A.S. Van Mooy, 2016, "LOBSTAHS: An adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers," in review, Anal. Chem.

Users should note that the version of the ptH2O2lipids LOBSet in this package does not include any PUA identifications.

.mzXML and .raw data files

The .mzXML and Thermo (.raw) data files from which the objects in the dataset were created are not included in the `PtH2O2lipids` library due to their very large size.

• The converted and centroided .mzXML files can be downloaded from PtH2O2lipids/mzXML
• The original Thermo .raw files and some metadata can be accessed at http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529.

Installation

Install all dependencies except LOBSTAHS

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("CAMERA")
BiocManager::install("xcms")

Install RTools

For windows: Download and install RTools from http://cran.r-project.org/bin/windows/Rtools/

For Unix: Install the R-development-packages (r-devel or r-base-dev)

Install packages needed for installation from Github:

install.packages("devtools")

Install LOBSTAHS

library("devtools")
install_github("vanmooylipidomics/LOBSTAHS")

Install 'PtH2O2lipids,' containing example data & xsAnnotate object

## install dataset 'PtH2O2lipids'
## see LOBSTAHS documentation for examples

install_github("vanmooylipidomics/PtH2O2lipids")