bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: O22
Oral presentation
10th Benelux Bioinformatics Conference bbc 2015
O22. PEPSHELL: VISUALIZATION OF CONFORMATIONAL PROTEOMICS
DATA
Elien Vandermarliere 1,2* , Davy Maddelein 1,2 , Niels Hulstaert 1,2 , Elisabeth Stes 1,2 , Michela Di Michele 1,2 ,
Kris Gevaert 1,2 , Edgar Jacoby 3 , Dirk Brehmer 3 & Lennart Martens 1,2 .
Department of Medical Protein Research, VIB 1 ; Department of Biochemistry, Ghent University 2 ; Oncology Discovery,
Janssen Research and Development – Janssen Pharmaceutica, Beerse 3 . * elien.vandermarliere@ugent.be
Proteins are dynamic molecules; they undergo crucial conformational changes induced by post-translational
modifications and by binding of cofactors or other molecules. The characterization of these conformational changes and
their relation to protein function is a central goal of structural biology. Unfortunately, most conventional methods to
obtain structural information do not provide information on protein dynamics. Therefore, mass spectrometry-based
approaches, such as limited proteolysis, hydrogen-deuterium exchange, and stable-isotope labelling, are frequently used
to characterize protein conformation and dynamics, yet the interpretation of these data can be cumbersome and time
consuming. Here, we present PepShell, a tool that allows interactive data analysis of mass spectrometry-based
conformational proteomics studies by visualization of the identified peptides both at the sequence and structure levels.
Moreover, PepShell allows the comparison of experiments under different conditions which include proteolysis times or
binding of the protein to different substrates or inhibitors.
INTRODUCTION
The study of protein structure with mass spectrometry,
called conformational proteomics, is frequently used to
characterize protein conformations and dynamics. Most of
these methods exploit the surface accessibility of amino
acids within the native protein conformation or more
specifically, the differences in protein surface accessibility
in different situations within a protein structure.
The experimental setup and subsequent workflow of a
conformational proteomics experiment do not deviate
drastically from that of a classic mass spectrometry-based
experiment in which peptides present in a complex peptide
mixture are identified. The final outcome of a
conformational proteomics experiment is a list of peptides.
These peptide lists typically span multiple experimental
conditions across which the structural observations are to
be compared; the peptide lists have to be combined and, if
available, mapped onto the structure of the protein.
To fulfill these latter steps, we developed PepShell
(Vandermarliere et al., 2015), to guide the interpretation
of mass spectrometry-based proteomics data in the context
of protein structure and dynamics.
TOOL DESCRIPTION
PepShell aids the user in the interpretation of the outcome
of conformational proteomics experiments and is
composed of three panels: the experiment comparison
panel, the PDB view panel, and the statistics panel.
The data to analyze
PepShell allows the input from limited proteolysis,
hydrogen-deuterium exchange, MS footprinting and
stable-isotope labelling experiments. The data have to
be present in a comma-separated text file format. The
project selection interface allows the user to select a
reference project and to indicate which setups need to
be compared with each other.
Experiment comparison
This panel allows the comparison of the selected
experimental setups at the sequence level. For each
experimental condition, the identified and quantified
peptides are mapped onto the sequence of the protein
of interest.
The PDB view panel
Here, the detected peptides are mapped on the protein
structure. The main requirement is the availability of a
3D structure of the protein of interest.
Statistics within PepShell
In this panel, the peptides of interest can be analyzed
in more detail. The outcome from CP-DT (Fannes et
al., 2013) for tryptic cleavage probability for each
tryptic cleavage position is given. Also detailed
comparison of the peptide ratios over the different
experimental setups is allowed.
CONCLUSIONS
The increasing popularity of structural proteomics is in
stark contrast with the availability of efficient tools to
visualize this multitude of data. There are however some
tools available that aid data interpretation; but these are
approach-specific and are aimed primarily at mass
spectrometrists with a specific focus on the experimental
mass spectrometry data and their processing and
interpretation. PepShell on the other hand is intended to
support downstream users to interpret the results obtained
from a variety of conformational proteomics approaches.
PepShell uses the peptide lists to compare different
experimental conditions and allows the visualization of
these differences onto the structure of the protein. As such,
PepShell bridges the gap between mass spectrometrybased
proteomics data and their interpretation in the
context of protein structure and dynamics.
PepShell is an open source Java application. Its binaries,
source code and documentation can be found at:
compomics.github.io/projects/pepshell.html
REFERENCES
Fannes T et al. J Proteome Res 12, 2253-2259 (2013).
Vandermarliere E et al. J Proteome Res 14, 1987-1990 (2015).
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