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Title: Xilmass: a new approach towards the identification of cross-linked peptides
Authors: Yılmaz, Şule
Drepper, Friedel
Hulstaert, Niels
Cernic, Masa
Gevaert, Kris
Economou, Anastassios
Warscheid, Bettina
Vandermarliere, Elien # ×
Issue Date: Oct-2016
Series Title: Analytical Chemistry vol:88 pages:9949-9957
Abstract: Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient ones. Moreover, cross-linking complements several structure determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in the search database such that the cross-linking sites are explicitly encoded, and (ii) the scoring function derived from the Andromeda algorithm was adapted to score against a theoretical MS/MS spectrum that contains the peaks from all possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was evaluated against the recently published Kojak and the popular pLink algorithms on a calmodulin-plectin complex data set, as well as three additional, published data sets. The results show that Xilmass typically had the highest number of identified distinct cross-linked sites and also the highest number of predicted cross-linked sites.
URI: 
ISSN: 0003-2700
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Molecular Bacteriology (Rega Institute)
× corresponding author
# (joint) last author

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