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Are neutral loss and internal product ions useful for top-down protein identification?
Xiao, Kaijie; Yu, Fan; Fang, Houqin; Xue, Bingbing; Liu, Yan; Li, Yunhui; Tian, Zhixin.
Afiliação
  • Xiao K; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
  • Yu F; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
  • Fang H; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
  • Xue B; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
  • Liu Y; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
  • Li Y; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
  • Tian Z; School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China. Electronic address: zhixintian@tongji.edu.cn.
J Proteomics ; 160: 21-27, 2017 05 08.
Article em En | MEDLINE | ID: mdl-28336331
Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear. Here we report our proteome-level utility benchmarking of neutral loss and internal product ions with tandem mass spectra of intact E. coli proteome. Utility of internal product ions was further evaluated at the protein level using selected tandem mass spectra of individual E. coli proteins. We found that both neutral loss and internal products ions do not have direct utility for protein identification when they were used for scoring of P Score; but they do have indirect utility for provision of more canonical b/y ions when they are included in the database search and overlapping ions between different ion types are resolved. BIOLOGICAL SIGNIFICANCE: Tandem mass spectrometry has evolved to be a state-of-the-art method for characterization of protein primary structures (including amino acid sequence, post-translational modifications (PTMs) as well as their site location), where full study and utilization tandem mass spectra and product ions are indispensable. This primary structure information is essential for higher order structure and eventual function study of proteins.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteoma / Escherichia coli / Espectrometria de Massas em Tandem Tipo de estudo: Diagnostic_studies / Prognostic_studies Idioma: En Ano de publicação: 2017 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteoma / Escherichia coli / Espectrometria de Massas em Tandem Tipo de estudo: Diagnostic_studies / Prognostic_studies Idioma: En Ano de publicação: 2017 Tipo de documento: Article