PepShell: visualization of conformational proteomics data.
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 labeling, 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, including different proteolysis times or binding of the protein to different substrates or inhibitors.
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Elien
E
Vandermarliere
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Davy
D
Maddelein
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Niels
N
Hulstaert
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Elisabeth
E
Stes
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Michela
M
Di Michele
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Kris
K
Gevaert
§Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium.
Edgar
E
Jacoby
§Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium.
Dirk
D
Brehmer
†Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Lennart
L
Martens
D003626:Data Display; D013058:Mass Spectrometry / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
D011506:Proteins
Comparison of peptides; PepShell; conformational proteomics; protein structure; visualization of peptides