title: Repeatability and reproducibility of product ion abundances in electron capture dissociation  mass spectrometry of peptides.
abstract: Site-specific reproducibility and repeatability of electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) are of fundamental importance for product ion abundance (PIA)-based peptide and protein structure analysis. However, despite the growing interest in ECD PIA-based applications, these parameters have not yet been investigated in a consistent manner. Here, we first provide a detailed description of the experimental parameters for ECD-based tandem mass spectrometry performed on a hybrid linear ion trap (LTQ) FT-ICR MS. In the following, we describe the evaluation and comparison of ECD and infrared multiphoton dissociation (IRMPD) PIA methodologies upon variation of a number of experimental parameters,  for example, cathode potential (electron energy), laser power, electron and photon irradiation periods and pre- irradiation delays, as well as precursor ion number. Ranges of experimental parameters that yielded an average PIA variation below 5% and 15% were determined for ECD and IRMPD, respectively. We report cleavage site-dependent ECD PIA variation below 20% and correlation coefficients between fragmentation patterns superior to 0.95 for experiments performed on three FT-ICR MS instruments. Overall, the encouraging results obtained for ECD PIA reproducibility and repeatability support the use of ECD PIA as a complementary source of information to m/z data in radical-induced dissociation applied for peptide and protein structure analysis.
authors: Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors: Hisham
authors: H
authors: Ben Hamidane
authors: Aleksey
authors: A
authors: Vorobyev
authors: Yury O
authors: YO
authors: Tsybin
mesh_terms: D000595:Amino Acid Sequence; D017357:Cyclotrons; D004583:Electrons; D005583:Fourier Analysis; D007477:Ions / Q000737:chemistry*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis*; D017785:Photons; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D015203:Reproducibility of Results; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins