Analysis of Label-Based Quantitative Proteomics Data Using IsoProt

Johannes Griss*, Veit Schwämmle

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review


Isobaric labeling has become an essential method for quantitative mass spectrometry based experiments. This technique allows high-throughput proteomics while providing reasonable coverage of protein measurements across multiple samples. Here, the analysis of isobarically labeled mass spectrometry data with a special focus on quality control and potential pitfalls is discussed. The protocol is based on our fully integrated IsoProt workflow. The concepts discussed are nevertheless applicable to the analysis of any isobarically labeled experiment using alternative computational tools and algorithms.

Original languageEnglish
Title of host publicationProteomics Data Analysis
EditorsDaniela Cecconi
Place of PublicationNew York
PublisherHumana Press
Publication date2021
ISBN (Print)978-1-0716-1640-6, 978-1-0716-1643-7
ISBN (Electronic)978-1-0716-1641-3
Publication statusPublished - 2021
SeriesMethods in Molecular Biology

Bibliographical note

Publisher Copyright:
© 2021, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.


  • Bioinformatics
  • Isobaric labeling
  • IsoProt
  • iTRAQ
  • Mass spectrometry
  • Quantitative proteomics
  • TMT


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