Abstract

Modern mass spectrometry-based proteomics enables the identification and quantification of thousands of proteins. Therefore, quantitative mass spectrometry represents an indispensable technology for biological and clinical research. Statistical analyses are required for the unbiased answering of scientific questions and to uncover all important information in the proteomic data. Classical statistical approaches and methods from other omics technologies are not ideal because they do not take into account the speciality of mass spectrometry data that include several thousands of proteins but often only a few dozens of samples (referred to as ‘curse of dimensionality’) and stochastic data properties that reflect sample preparation and spectral acquisition (Choi 2014).

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• How to perform label-free shotgun (DDA) data analysis in MaxQuant and MSstats?
• Which proteins are differentially abundant in the two types of cutaneous squamous cell carcinomas?

Learning Objectives

• Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data