title: Fragmentation features of intermolecular cross-linked peptides using N-hydroxy- succinimide esters by MALDI- and ESI-MS/MS for use in structural proteomics.
abstract: The use of mass spectrometry coupled with chemical cross-linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross-linked peptides. The interpretation of the MS/MS data generated in cross-linking experiments using N-hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross-linked peptides occur when two different peptides are connected by the cross-linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross-linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross-linked peptides present in cross-linking experiments and be further implemented in search engine's algorithms.
authors.affiliation: Institute of Chemistry, University of Campinas, CP 6154 Campinas, SP 13083-970, Brazil.
authors.forename: Luiz F A
authors.initials: LF
authors.lastname: Santos
authors.forename: Amadeu H
authors.initials: AH
authors.lastname: Iglesias
authors.forename: Fabio C
authors.initials: FC
authors.lastname: Gozzo
mesh_terms: D003432:Cross-Linking Reagents / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D013388:Succinimides / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D003432:Cross-Linking Reagents; D010446:Peptide Fragments; D013388:Succinimides; C001426:N-hydroxysuccinimide