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The interpretation of the MS\/MS data generated in cross\u2010linking experiments using N\u2010hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross\u2010linked peptides occur when two different peptides are connected by the cross\u2010linker 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\u2010linked 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\u2010linked peptides present in cross\u2010linking experiments and be further implemented in search engine's algorithms. Copyright \u00a9 2011 John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/jms.1951","type":"journal-article","created":{"date-parts":[[2011,7,17]],"date-time":"2011-07-17T22:18:55Z","timestamp":1310941135000},"page":"742-750","source":"Crossref","is-referenced-by-count":17,"title":["Fragmentation features of intermolecular cross\u2010linked peptides using N\u2010hydroxy\u2010 succinimide esters by MALDI\u2010 and ESI\u2010MS\/MS for use in structural proteomics"],"prefix":"10.1002","volume":"46","author":[{"given":"Luiz F. 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