title: Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis.
abstract: CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .
authors.affiliation: Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany, michael.goetze@biochemtech.uni-halle.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Götze
authors.forename: Jens
authors.initials: J
authors.lastname: Pettelkau
authors.forename: Romy
authors.initials: R
authors.lastname: Fritzsche
authors.forename: Christian H
authors.initials: CH
authors.lastname: Ihling
authors.forename: Mathias
authors.initials: M
authors.lastname: Schäfer
authors.forename: Andrea
authors.initials: A
authors.lastname: Sinz
mesh_terms: D003432:Cross-Linking Reagents; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D003432:Cross-Linking Reagents; D011506:Proteins