Proteomics

Dataset Information

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


ABSTRACT: Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient interactions. 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 a novel way in the search database that explicitly encodes cross-linking sites and (ii) the scoring function from the Andromeda algorithm was adapted to score against a theoretical MS spectrum that contains the peaks from all the possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was subsequently evaluated against the recently published Kojak and the popular pLink algorithms on a data set that contains calmodulin-plectin.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Sule Yilmaz  

LAB HEAD: Lennart Martens

PROVIDER: PXD003880 | Pride | 2016-09-27

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
QEplus009907.mgf Mgf
QEplus009907.raw Raw
QEplus009907_Kojakv136.txt Txt
QEplus009907_percolator_dfMods_Th003_corrected-Inter.txt Txt
QEplus009907_percolator_dfMods_Th003_corrected-Intra.txt Txt
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Publications

Xilmass: A New Approach toward the Identification of Cross-Linked Peptides.

Yılmaz Şule Ş   Drepper Friedel F   Hulstaert Niels N   Černič Maša M   Gevaert Kris K   Economou Anastassios A   Warscheid Bettina B   Martens Lennart L   Vandermarliere Elien E  

Analytical chemistry 20160928 20


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 structural 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  ...[more]

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