Mass spectrometry data processing

Day 1: Protein identification

Training material

• Slides
• Tutorial on peptide spectrum matching
• Material for peptide spectrum matching
• Tutorial on interpreting the identification results
• Material for interpreting the identification results
• Tutorial on peptide and protein validation
• Answers to the questions asked in the tutorials

Software

• Latest version of 64-bit Java
• SearchGUI
• PeptideShaker

Day 2: Protein quantification

Training material

• Slides on Identification evaluation and Target decoy approach
• Tutorial on Evaluating target decoy quality
• Slides on Preprocessing
• Slides on Preprocessing results
• Tutorial on Preprocessing with MSqRob for simple designs
• Robust regression explained by example
• Slides on Statistical inference
• Tutorial on Statistical analysis with MSqRob for factorial designs

Software

• Latest version of R
• RStudio
• RTools only Windows users need this
• R packages: run RStudio as administrator and type:
  

  install.packages("devtools")
  library(devtools)
  source("http://bioconductor.org/biocLite.R")
  biocLite() 
  biocLite("MSnbase") 
  devtools::install_github("statOmics/MSqRob@MSqRob0.7.5")
  library(MSqRob)

• Download and unzip pda master tree:
  Go to the pda site on github
  Click on the clone/download button and select download zip
  Unzip the repository
  Open Rstudio and go to the unzipped folder
• Data
  

Issues with installation of R/R packages

Mac: error message: Setting LC_CTYPE failed, using “C” during package installation

• Close RStudio
• Open Terminal
• Type:

  defaults write org.R-project.R force.LANG en_US.UTF-8

• Close Terminal
• Start RStudio and retry installation