title: Assignment of disulfide-linked peptides using automatic a1 ion recognition.
abstract: We present a novel approach for the assignment of peptides containing disulfide linkages. Dimethyl labeling is introduced to generate labeled peptides which exhibit enhanced a1 ion signals during MS/MS fragmentation. For disulfide-linked peptides, multiple a1 ions can be observed due to multiple N-termini. This distinct feature allows sieving out the disulfide-linked peptides; meanwhile, the N-terminal amino acids can be identified. With such information, the number of possible peptide combinations involved in a disulfide bond dramatically narrows down. Furthermore, we developed a computational algorithm to perform target a1 ion screening followed by molecular weight matching of cysteine-containing peptides with specific amino acids at the N-termini. Once the protein sequence and the peak list from a LC-MS/MS survey scan of labeled peptides are imported, the identities of disulfide-linked peptides can be readily obtained. The presented approach is simple and straightforward, offering a valuable tool for protein structural characterization.
authors: Life Science Business Unit and Computer Integrated Manufacturing Business Unit, C Sun MFG. LTD., 7F.-9, No.79, Sec. 1, Sintai Fifth Road, Sijhih City, Taipei County 221, Taiwan. cindyhuang@csun.com.tw
authors: Sheng Yu
authors: SY
authors: Huang
authors: Chien Hsien
authors: CH
authors: Wen
authors: Ding Tzai
authors: DT
authors: Li
authors: Jue Liang
authors: JL
authors: Hsu
authors: Chinpan
authors: C
authors: Chen
authors: Fong Ku
authors: FK
authors: Shi
authors: Yueh Yi
authors: YY
authors: Lin
mesh_terms: D000465:Algorithms; D000951:Antigens, Neoplasm / Q000032:analysis* / Q000737:chemistry; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000737:chemistry; D004220:Disulfides / Q000032:analysis* / Q000737:chemistry; D006801:Humans; D037181:Lectins, C-Type / Q000032:analysis* / Q000737:chemistry; D008745:Methylation; D000073718:Pancreatitis-Associated Proteins; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011994:Recombinant Proteins / Q000032:analysis / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000191:economics / Q000379:methods*
chemical_list: D000951:Antigens, Neoplasm; D014408:Biomarkers, Tumor; D004220:Disulfides; D037181:Lectins, C-Type; D000073718:Pancreatitis-Associated Proteins; D010455:Peptides; C000612141:REG3A protein, human; D011994:Recombinant Proteins