StavroX--a software for analyzing crosslinked products in protein interaction studies.
Chemical crosslinking in combination with mass spectrometry has matured into an alternative approach to derive low-resolution structural information of proteins and protein complexes. Yet, one of the major drawbacks of this strategy remains the lack of software that is able to handle the large MS datasets that are created after chemical crosslinking and enzymatic digestion of the crosslinking reaction mixtures. Here, we describe a software, termed StavroX, which has been specifically designed for analyzing highly complex crosslinking datasets. The StavroX software was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. We show that the StavroX software is advantageous for analyzing crosslinked products due to its easy-to-use graphical user interface and the highly automated analysis of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data resulting in short times for analysis. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.
Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
Michael
M
Götze
Jens
J
Pettelkau
Sabine
S
Schaks
Konstanze
K
Bosse
Christian H
CH
Ihling
Fabian
F
Krauth
Romy
R
Fritzsche
Uwe
U
Kühn
Andrea
A
Sinz
D000465:Algorithms; D000818:Animals; D002417:Cattle; D003432:Cross-Linking Reagents / Q000737:chemistry; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface
D003432:Cross-Linking Reagents; D011506:Proteins