An improved workflow for identifying ubiquitin/ubiquitin-like protein conjugation sites from tandem mass spectra

作者：Xu, Changming; Zhang, Jiyang; Zhang, Wei; Liu, Hui; Fang, Jianwei; Xie, Hongwei^*

来源：Proteomics, 2013, 13(17): 2579-2584.

DOI：10.1002/pmic.201300151

• Bioinformatics
• Tandem mass spectra
• Ubiquitin
• Ubiquitin-like proteins
• Workflow

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.

• 出版日期2013-9
• 单位中国人民解放军国防科学技术大学