title: Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition.
abstract: Many software tools have been developed for analyzing stable isotope labeling (SIL)-based quantitative proteomic data using data dependent acquisition (DDA). However, programs for analyzing SIL-based quantitative proteomics data obtained with data independent acquisition (DIA) have yet to be reported. Here, we demonstrated the development of a new software for analyzing SIL data using the DIA method. Performance of the DIA on SYNAPT G2MS was evaluated using SIL-labeled complex proteome mixtures with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10) and compared with the DDA on linear ion trap (LTQ)-Orbitrap MS. The DIA displays relatively high quantitation accuracy for peptides cross all intensity regions, while the DDA shows an intensity dependent distribution of H/L ratios. For the three proteome mixtures, the number of detected SIL-peptide pairs and dynamic range of protein intensities using DIA drop stepwise, whereas no significant changes in these aspects using DDA were observed. The new software was applied to investigate the proteome difference between mouse embryonic fibroblasts (MEFs) and MEF-derived induced pluripotent stem cells (iPSCs) using (16)O/(18)O labeling. Our study expanded the capacities of our UNiquant software pipeline and provided valuable insight into the performance of the two cutting-edge MS platforms for SIL-based quantitative proteomic analysis today.
authors.affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.
authors.forename: Xin
authors.initials: X
authors.lastname: Huang
authors.forename: Miao
authors.initials: M
authors.lastname: Liu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Nold
authors.forename: Changhai
authors.initials: C
authors.lastname: Tian
authors.forename: Kai
authors.initials: K
authors.lastname: Fu
authors.forename: Jialin
authors.initials: J
authors.lastname: Zheng
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Geromanos
authors.forename: Shi-Jian
authors.initials: SJ
authors.lastname: Ding
mesh_terms: D000818:Animals; D002460:Cell Line; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D005347:Fibroblasts / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism; D007553:Isotope Labeling / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D051379:Mice; D010103:Oxygen Isotopes / Q000737:chemistry; D010455:Peptides / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D010103:Oxygen Isotopes; D010455:Peptides; D020543:Proteome