StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies

• Published in: Journal of the American Society for Mass Spectrometry Vol. 23; no. 1; pp. 76 - 87
• Main Authors: Götze, Michael, Pettelkau, Jens, Schaks, Sabine, Bosse, Konstanze, Ihling, Christian H., Krauth, Fabian, Fritzsche, Romy, Kühn, Uwe, Sinz, Andrea
• Format: Journal Article
• Language: English
• Published: New York Springer-Verlag 01.01.2012; Elsevier; Springer Nature B.V
• Subjects: Algorithms; Analytical Chemistry; Analytical, structural and metabolic biochemistry; Animals; Bioinformatics; Biological and medical sciences; Biotechnology; Calmodulin; Cattle; Chemistry; Chemistry and Materials Science; Cross-Linking Reagents - chemistry; Crosslinking; Databases, Protein; Datasets; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Graphical user interface; Ions; Laminin; Mass spectrometry; Mass Spectrometry - methods; Mice; Organic Chemistry; Protein Interaction Mapping - methods; Proteins; Proteins - chemistry; Proteins - metabolism; Proteomics; Research Article; Scientific imaging; Software; Spectroscopy; Tandem Mass Spectrometry; User-Computer Interface; Enzymatic digestion; Data analysis; Chemical crosslinking; Software; Mass spectrometry; Protein complexes; Tandem mass spectrometry; Enzymatic hydrolysis; Crosslinking; Protein
• ISSN: 1044-0305; 1879-1123
• DOI: 10.1007/s13361-011-0261-2

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.