title: An improved workflow for identifying ubiquitin/ubiquitin-like protein conjugation sites from tandem mass spectra.
abstract: The identification of ubiquitin (Ub) and Ub-like protein (Ubl) conjugation sites is important in understanding their roles in biological pathway regulations. However, unambiguously and sensitively identifying Ub/Ubl conjugation sites through high-throughput MS remains challenging. We introduce an improved workflow for identifying Ub/Ubl conjugation sites based on the ChopNSpice and X!Tandem software. ChopNSpice is modified to generate Ub/Ubl conjugation peptides in the form of a cross-link. A combinatorial FASTA database can be acquired using the modified ChopNSpice (MchopNSpice). The modified X!Tandem (UblSearch) introduces a new fragmentation model for the Ub/Ubl conjugation peptides to match unambiguously the MS/MS spectra with linear peptides or Ub/Ubl conjugation peptides using the combinatorial FASTA database. The novel workflow exhibited better performance in analyzing an Ub and Ubl spectral library and a large-scale Trypanosoma cruzi small Ub-related modifier dataset compared with the original ChopNSpice method. The proposed workflow is more suitable for processing large-scale MS datasets of Ub/Ubl modification. MchopNSpice and UblSearch are freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/maublsearch.
authors.affiliation: College of Mechatronic Engineering and Automation, National University of Defense Technology, Changsha, P. R. China.
authors.forename: Changming
authors.initials: C
authors.lastname: Xu
authors.forename: Jiyang
authors.initials: J
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Jianwei
authors.initials: J
authors.lastname: Fang
authors.forename: Hongwei
authors.initials: H
authors.lastname: Xie
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D011485:Protein Binding; D015800:Protozoan Proteins / Q000032:analysis / Q000378:metabolism; D020539:Sequence Analysis, Protein / Q000379:methods*; D025841:Small Ubiquitin-Related Modifier Proteins / Q000032:analysis / Q000378:metabolism*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000706:statistics & numerical data; D014349:Trypanosoma cruzi / Q000378:metabolism; D025801:Ubiquitin / Q000032:analysis / Q000378:metabolism*; D057188:Workflow
chemical_list: D015800:Protozoan Proteins; D025841:Small Ubiquitin-Related Modifier Proteins; D025801:Ubiquitin
keywords: Bioinformatics; Tandem mass spectra; Ubiquitin; Ubiquitin-like proteins; Workflow