title: Mass defect-based pseudo-isobaric dimethyl labeling for proteome quantification.
abstract: Discovering differentially expressed proteins in various biological samples requires proteome quantification methods with accuracy, precision, and wide dynamic range. This study describes a mass defect-based pseudo-isobaric dimethyl labeling (pIDL) method based on the subtle mass defect differences between (12)C/(13)C and (1)H/(2)H. Lys-C protein digests were labeled with CD2O/(13)CD2O and reduced with NaCNBD3/NaCNBH3 as heavy and light isotopologues, respectively. The fragment ion pairs with mass differences of 5.84 mDa were resolved by high-resolution tandem mass spectrometry (MS/MS) and used for quantification. The pIDL method described here resulted in highly accurate and precise quantification results with approximately 100-fold dynamic range. Furthermore, the pIDL method was extended to 4-plex proteome quantification and applied to the quantitative analysis of proteomes from Hca-P and Hca-F, two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates.
authors.affiliation: National Chromatographic Research and Analysis Center, Key Lab of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Yichu
authors.initials: Y
authors.lastname: Shan
authors.forename: Qi
authors.initials: Q
authors.lastname: Wu
authors.forename: Shen
authors.initials: S
authors.lastname: Zhang
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhang
authors.forename: Yukui
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000818:Animals; D006528:Carcinoma, Hepatocellular / Q000378:metabolism; D007553:Isotope Labeling / Q000379:methods*; D008113:Liver Neoplasms / Q000378:metabolism; D008745:Methylation; D051379:Mice; D009363:Neoplasm Proteins / Q000378:metabolism*; D010446:Peptide Fragments / Q000032:analysis* / Q000378:metabolism; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014407:Tumor Cells, Cultured
chemical_list: D009363:Neoplasm Proteins; D010446:Peptide Fragments; D020543:Proteome