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PlexedPiper

R package used at PNNL for processing isobaric labeling (e.g. TMT) proteomics data. The key inputs are:

  • MS/MS identifications from the MS-GF+ search engine
  • Reporter ion intensities extracted using MASIC
  • Tables outlining study design
    • table linking dataset to plexes
    • table linking reporter channels with sample names
    • table identifying reference within each plex

Updates

Updates to this package are detailed in the NEWS.md file and in the releases.

Website

The PlexedPiper pkgdown website contains pre-built vignettes as well as updates and documentation.

R Installation and Usage 

if(!require("remotes", quietly = T)) install.packages("remotes")
remotes::install_github("PNNL-Comp-Mass-Spec/PlexedPiper", build_vignettes = TRUE)
library(PlexedPiper)
vignette("tmt_pipeline_v1")

Example Data

A companion R package with test data based on the MoTrPAC pilot study is available here

Docker/Linux installation

PlexedPiper can be run within a Docker Container

  • This example Dockerfile shows the required system libraries, starting with the base rocker/TidyVerse image
FROM rocker/tidyverse:3.6.1
RUN apt-get update \
 && apt-get install -y --no-install-recommends \
 unixodbc \
 unixodbc-dev \
 freetds-dev \
 freetds-bin \
 tdsodbc \
 libcurl4-openssl-dev \
 libxml2-dev \
 libnetcdf-dev \
 libssl-dev
RUN R -e 'remotes::install_github("PNNL-Comp-Mass-Spec/PlexedPiper", build_vignettes = TRUE)'

MacOS installation

On MacOS, install Homebrew, then use

brew install unixodbc
brew install freetds

Note, the --with-unixodbc option in freetds installation is deprecated.

Create ~/.odbcinst.ini file and add

[FreeTDS]
Driver = /usr/local/lib/libtdsodbc.so

If your location of libtdsodbc.so differs, use the proper location.

Installation Tips

If within PNNL network there may be an error associated with mount_smbfs. This happens due to network access credentials. Options are either to wait or proactively access one of the PNNL servers. For example try mounting one of the public directories from the terminal window. Enter your network password once requested. mount -t smbfs //protoapps/DataPkgs/Public/ ~/temp_msms_results Then compilation of the vignettes that imply access to PNNL DMS should proceed smoothly.

Original Location

The original location is on the vladpetyuk account, repo PlexedPiper.