Proteomics Data Analysis in R/Bioconductor

Tyler Sagendorf

May 27, 2022

Welcome!

This tutorial is very much a work-in progress. Even sections that appear finished are likely to be changed. I will update this when significant progress is made. Thank you for your patience.

It is highly recommended to review the resources below before continuing with the rest of the tutorial.

• Proteomics Overview
  • Protein Analysis by Shotgun/Bottom-up Proteomics
  • Modern Proteomics – Sample Preparation, Analysis and Practical Applications
  • Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects

• Mass Spectrometry

  • Warwick School of Life Sciences Teaching Animations
  • Tandem Mass Spectrometry for Peptide and Protein Sequence Analysis
  • Maestro: Comprehensive, Multi-Stage Spectrum Identification in Protein Mass Spectrometry
  • Searching databases for protein identification - part 1 (YouTube video)
  • Mass spectrometry for proteomics - part one (YouTube video)
  • Electrospray Ionisation Mass Spectrometry: Principles and Clinical Applications

• PNNL’s Data Management System (DMS)

• Integrative Omics PRISMWiki

• Universal Protein Resource (UniProt): protein sequence and annotation data

• False Discovery Rate (FDR)

  • How to talk about protein‐level false discovery rates in shotgun proteomics
  • Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin
  • False Discovery Rate: PEAKS FDR Estimation
  • False discovery rates in spectral identification

• RStudio Cheatsheets

• Pattern matching with regular expressions

  • R for Data Science: Strings
  • RegexOne: Learn Regular Expressions with simple, interactive exercises.