Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Standard

Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper. / Grimaud, Arthur; Haugaard Holck, Frederik; Buur, Louise Marie; Kirsch, Rebecca; Schwämmle, Veit.

Computational Methods for Predicting Post-Translational Modification Sites. Humana Press, 2022. p. 261-273 (Methods in Molecular Biology, Vol. 2499).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Harvard

Grimaud, A, Haugaard Holck, F, Buur, LM, Kirsch, R & Schwämmle, V 2022, Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper. in Computational Methods for Predicting Post-Translational Modification Sites. Humana Press, Methods in Molecular Biology, vol. 2499, pp. 261-273. https://doi.org/10.1007/978-1-0716-2317-6_13

APA

Grimaud, A., Haugaard Holck, F., Buur, L. M., Kirsch, R., & Schwämmle, V. (2022). Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper. In Computational Methods for Predicting Post-Translational Modification Sites (pp. 261-273). Humana Press. Methods in Molecular Biology Vol. 2499 https://doi.org/10.1007/978-1-0716-2317-6_13

Vancouver

Grimaud A, Haugaard Holck F, Buur LM, Kirsch R, Schwämmle V. Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper. In Computational Methods for Predicting Post-Translational Modification Sites. Humana Press. 2022. p. 261-273. (Methods in Molecular Biology, Vol. 2499). https://doi.org/10.1007/978-1-0716-2317-6_13

Author

Grimaud, Arthur ; Haugaard Holck, Frederik ; Buur, Louise Marie ; Kirsch, Rebecca ; Schwämmle, Veit. / Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper. Computational Methods for Predicting Post-Translational Modification Sites. Humana Press, 2022. pp. 261-273 (Methods in Molecular Biology, Vol. 2499).

Bibtex

@inbook{450219cbf32c4a2d9212c64d37ec53ad,
title = "Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper",
abstract = "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.",
keywords = "Cross talk, Epigenomics, Histones, Middle-down, Posttranslational modifications",
author = "Arthur Grimaud and {Haugaard Holck}, Frederik and Buur, {Louise Marie} and Rebecca Kirsch and Veit Schw{\"a}mmle",
note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2022",
doi = "10.1007/978-1-0716-2317-6_13",
language = "English",
isbn = "978-1-0716-2316-9",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "261--273",
booktitle = "Computational Methods for Predicting Post-Translational Modification Sites",
address = "United States",

}

RIS

TY - CHAP

T1 - Exploration of Protein Posttranslational Modification Landscape and Cross Talk with CrossTalkMapper

AU - Grimaud, Arthur

AU - Haugaard Holck, Frederik

AU - Buur, Louise Marie

AU - Kirsch, Rebecca

AU - Schwämmle, Veit

N1 - Publisher Copyright: © 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Cross talk

KW - Epigenomics

KW - Histones

KW - Middle-down

KW - Posttranslational modifications

U2 - 10.1007/978-1-0716-2317-6_13

DO - 10.1007/978-1-0716-2317-6_13

M3 - Book chapter

C2 - 35696085

AN - SCOPUS:85132890396

SN - 978-1-0716-2316-9

T3 - Methods in Molecular Biology

SP - 261

EP - 273

BT - Computational Methods for Predicting Post-Translational Modification Sites

PB - Humana Press

ER -

ID: 312698799