Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper

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  • Arthur Grimaud
  • Frederik Haugaard Holck
  • Louise Marie Buur
  • Kirsch, Rebecca
  • Veit Schwämmle

Post-translational modifications (PTMs) of proteins play crucial roles in defining protein function. They often do not occur alone, leading to a large variety of proteoforms that correspond to different combinations of multiple PTMs simultaneously decorating a protein. Changes of these proteoforms can be quantified via middle-down and top-down mass spectrometry experiments where the simultaneous PTM settings are obtained by measuring long peptides or entire proteins. Data from such experiments poses big challenges in identifying relevant features of biological and clinical importance. Generally, multiple data layers need to be considered such as proteoforms, individual PTMs, and PTM types. Therein, visualization methods are a crucial part of data analysis as they provide, if applied correctly, insights into both general behaviors as well as a deep view into fine-grained behavior. Here, we present a workflow to visualize histone proteins and their myriad of PTMs based on different R visualization modules applied to data from quantitative middle-down experiments. The procedure can be adapted to diverse experimental designs and is applicable to different proteins and PTMs.

Original languageEnglish
Title of host publicationComputational Methods for Predicting Post-Translational Modification Sites
PublisherHumana Press
Publication date2022
ISBN (Print)978-1-0716-2316-9
ISBN (Electronic)978-1-0716-2317-6
Publication statusPublished - 2022
SeriesMethods in Molecular Biology

Bibliographical note

Publisher Copyright:
© 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

    Research areas

  • Cross talk, Epigenomics, Histones, Middle-down, Posttranslational modifications

ID: 312698799