e-learning

MaxQuant and MSstats for the analysis of TMT data

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Abstract

In this training we will cover the full analysis workflow from tandem mass tag (TMT) labeled samples using MaxQuant in conjunction with MSstatsTMT.

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 analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?
  • Which proteins are differentially abundant between KMT9α knock-down and control cells?

Learning Objectives

  • Learn how to use MaxQuant and MSstats for the analysis of TMT labelled shotgun (DDA) data
  • Learn how to create an experimental design template for fractionated data in MaxQuant
  • Learn how to create an annotation file for MSstatsTMT

Licence: Creative Commons Attribution 4.0 International

Keywords: DDA, Proteomics, TMT

Target audience: Students

Resource type: e-learning

Version: 10

Status: Active

Prerequisites:

Introduction to Galaxy Analyses

Learning objectives:

  • Learn how to use MaxQuant and MSstats for the analysis of TMT labelled shotgun (DDA) data
  • Learn how to create an experimental design template for fractionated data in MaxQuant
  • Learn how to create an annotation file for MSstatsTMT

Date modified: 2023-11-09

Date published: 2021-08-13

Authors: Klemens Fröhlich, Matthias Fahrner, Melanie Föll

Contributors: Klemens Fröhlich, Matthias Fahrner, Melanie Föll

Scientific topics: Proteomics

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