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J Am Soc Mass Spectrom. 2015 Jan;26(1):83-97. doi: 10.1007/s13361-014-1001-1. Epub 2014 Sep 27.

Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis.

Author information

1
Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany, michael.goetze@biochemtech.uni-halle.de.

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 .

PMID:
25261217
DOI:
10.1007/s13361-014-1001-1
[Indexed for MEDLINE]

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