Universität zu Köln

Goetze, Michael, Pettelkau, Jens, Fritzsche, Romy, Ihling, Christian H., Schaefer, Mathias ORCID: 0000-0002-5943-4335 and Sinz, Andrea (2015). Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis. J. Am. Soc. Mass Spectrom., 26 (1). S. 83 - 98. NEW YORK: SPRINGER. ISSN 1879-1123

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Goetze, Michael UNSPECIFIED UNSPECIFIED UNSPECIFIED Pettelkau, Jens UNSPECIFIED UNSPECIFIED UNSPECIFIED Fritzsche, Romy UNSPECIFIED UNSPECIFIED UNSPECIFIED Ihling, Christian H. UNSPECIFIED UNSPECIFIED UNSPECIFIED Schaefer, Mathias UNSPECIFIED orcid.org/0000-0002-5943-4335 UNSPECIFIED Sinz, Andrea UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-418111
DOI:	10.1007/s13361-014-1001-1
Journal or Publication Title:	J. Am. Soc. Mass Spectrom.
Volume:	26
Number:	1
Page Range:	S. 83 - 98
Date:	2015
Publisher:	SPRINGER
Place of Publication:	NEW YORK
ISSN:	1879-1123
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Chemistry > Institute of Organic Chemistry
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language MASS-SPECTROMETRIC ANALYSIS; FRAGMENTATION REACTIONS; IDENTIFICATION; REAGENT; SOFTWARE; ARCHITECTURE; CONSTRAINTS; CHAPERONIN; PRODUCTS; BEHAVIOR Multiple languages Biochemical Research Methods; Chemistry, Analytical; Chemistry, Physical; Spectroscopy Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/41811