PeptidoformVisualisation: a Shiny app to visualise the

intensity patterns of different peptidoforms

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BACKGROUND & METHODS WHAT’S NEW?

The lack of open source, freely available visualisation and preprocessing tools to We developed a Shiny app
visualise (histone- related) peptidoforms is a missed opportunity to make the most out sse visualises peptidoform-level
of histone post translational modification (hPTM) data. intensity data. This app has been
made to accompany the largest
Drugs that target epigenetic mechanisms like histone posttranslational modifications (hPTMs), called histone atlas to date for T-ALL cells,
epidrugs, can be used in clinical trials trying to reprogram the epigenetic landscape in the cancer but any peptidoform data can be
epigenome. This holds great promise in patient care to prevent disease states. Nonetheless, the mapping of uploaded.
hPTMs, with the aid of mass spectrometry based proteomics (MS) has not been extensively described.
Therefore, we have made the first untargeted map of the histone code for 21 T-cell acute lymphoblastic
leukaemia cell lines. However, extracting biological information from this map is not trivial because of the
WHERE TO FIND?
complexity of the histone code1-2. Because of this, data sharing and reuse is important to facilitate transfer
[Link]
of knowledge and information. We have pre-processed the raw data into a single platform-independent eom
The data:
Progenesis QIP project that is fully accessible so that other researchers can use this browsable template.
Because data visualisation and pre-processing are important first steps when analysing data but are often [Link]/cgi/GetDatas
not trivial for biologists without programming experience, we have developed an accompanying Shiny app et?ID= PXD031500
in which users can intuitively visualise the different peptidoforms present in the dataset. The app:
This Shiny app, called PeptidoformVisualisation, is an interactive web app developed with the [Link]
Paper: mics/
Shiny R Package ([Link] version 1.7.1). The app and installation instructions can be
PeptidoformViz
found via the link on the right.
THE APP – tab 1 [Link]
10.1101/2022.
&2 05.05.490796

The app currently consists of

three main panels: data
import, pre- processing and
visualization. There are help
buttons everywhere to assist
the user. The data input tab
requires a file that contains
peptide level intensity data
and a corresponding
metadata file containing at
least enough information so
that each row represents one
unique ID. In the pre-
processing tab the user can
opt for several pre-
processing steps:
logarithmictransformation,
normalization and a
filtering step based on
missing intensity values. A
density plot and boxplot of
the data are generated to aid
the user in this decision. and
a filtering step based on
missing intensity values. A THE APP – tab 3
density plot and boxplot of After the pre-processing, the user can go on to
the data are generated to aid the visualization panel. Here we work with
the user in this decision. the peptidoforms of one protein only.
Accordingly, the user can select a protein of
interest present in the dataset via a dropdown
menu. A data table is displayed containing all
peptidoforms of the selected protein and
corresponding intensity values. It is possible to
search for certain patterns in peptide sequences
in the table, e.g., a present modification or a
certain sequence. Two figures are rendered
based on the data in the displayed data
table: a boxplot and a line plot of all the
peptidoforms. It is possible to highlight
peptidoforms of interest by clicking on them in
the data table. The corresponding line(s) in the
lineplot will then be highlighted, and
corresponding dots will appear in the boxplot.
The data table and figures can be downloaded to
the user’s computer. downloa downloaded to the
user’s [Link] to the user’s computer.
downloaded to the user’s computer. downloaded
to the user’s computer. downloaded to the user’s
WHAT’S NEXT? GET I N computer.
Because of the nature of Shiny apps and how they TOUCH
are developed, it is quite easy to add additional
features later on. In the future, we aim to extend the XXXDemeulemeester
functionalities of the Shiny app with advanced nixxxxxxxxxxxxxxxxxxxxxxxx
statistical analyses, including single PTM level
quantification.

References
1. Huang, H., Sabari, B. R., Garcia, B. A., Allis, C. D. & Zhao, Y. SnapShot: Histone Modifications. Cell 159, 458-458.e1 (2014). Thanks to:
Promotors:
2. Janssen, K. A., Sidoli, S. & Garcia, B. A. Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology. Methods Enzymol. 586, 359–378 (2017). Lien Provez, Laura Corveleyn, Prof. Dr. Lennart Martens
3. R Core Team. R: A language and environment for statistical computing. [Link] (2017). Bart Van Puyvelde, dr. Prof. Dr. Lieven Clement
4. RStudio Team. RStudio: Integrated Development Environment for R. [Link] (2021). Maarten Dhaenens