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Xilmass: a new approach toward the identification of cross-linked peptides

Sule Yilmaz-Rumpf UGent, Friedel Drepper, Niels Hulstaert UGent, Maša Černič, Kris Gevaert UGent, Anastassios Economou, Bettina Warscheid, Lennart Martens UGent and Elien Vandermarliere UGent (2016) ANALYTICAL CHEMISTRY. 88(20). p.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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
LINKING MASS-SPECTROMETRY, MAMMALIAN MITOCHONDRIAL RIBOSOME, PROTEIN-PROTEIN INTERACTIONS, STRUCTURAL BIOLOGY, PROTEOMICS, COMPLEXES, SOFTWARE, DATABASE, DISTANCES, TOOL
journal title
ANALYTICAL CHEMISTRY
Anal. Chem.
volume
88
issue
20
pages
9949 - 9957
Web of Science type
Article
Web of Science id
000385907400013
ISSN
0003-2700
DOI
10.1021/acs.analchem.6b01585
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
8110856
handle
http://hdl.handle.net/1854/LU-8110856
date created
2016-10-12 11:00:48
date last changed
2017-04-25 11:33:54
@article{8110856,
  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.},
  author       = {Yilmaz-Rumpf, Sule and Drepper, Friedel and Hulstaert, Niels and \v{C}erni\v{c}, Ma\v{s}a and Gevaert, Kris and Economou, Anastassios and Warscheid, Bettina and Martens, Lennart and Vandermarliere, Elien},
  issn         = {0003-2700},
  journal      = {ANALYTICAL CHEMISTRY},
  keyword      = {LINKING MASS-SPECTROMETRY,MAMMALIAN MITOCHONDRIAL RIBOSOME,PROTEIN-PROTEIN INTERACTIONS,STRUCTURAL BIOLOGY,PROTEOMICS,COMPLEXES,SOFTWARE,DATABASE,DISTANCES,TOOL},
  language     = {eng},
  number       = {20},
  pages        = {9949--9957},
  title        = {Xilmass: a new approach toward the identification of cross-linked peptides},
  url          = {http://dx.doi.org/10.1021/acs.analchem.6b01585},
  volume       = {88},
  year         = {2016},
}

Chicago
Yilmaz-Rumpf, Sule, Friedel Drepper, Niels Hulstaert, Maša Černič, Kris Gevaert, Anastassios Economou, Bettina Warscheid, Lennart Martens, and Elien Vandermarliere. 2016. “Xilmass: a New Approach Toward the Identification of Cross-linked Peptides.” Analytical Chemistry 88 (20): 9949–9957.
APA
Yilmaz-Rumpf, S., Drepper, F., Hulstaert, N., Černič, M., Gevaert, K., Economou, A., Warscheid, B., et al. (2016). Xilmass: a new approach toward the identification of cross-linked peptides. ANALYTICAL CHEMISTRY, 88(20), 9949–9957.
Vancouver
1.
Yilmaz-Rumpf S, Drepper F, Hulstaert N, Černič M, Gevaert K, Economou A, et al. Xilmass: a new approach toward the identification of cross-linked peptides. ANALYTICAL CHEMISTRY. 2016;88(20):9949–57.
MLA
Yilmaz-Rumpf, Sule, Friedel Drepper, Niels Hulstaert, et al. “Xilmass: a New Approach Toward the Identification of Cross-linked Peptides.” ANALYTICAL CHEMISTRY 88.20 (2016): 9949–9957. Print.