title: UNiquant, a program for quantitative proteomics analysis using stable isotope labeling.
abstract: Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.
authors.affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Huang
authors.forename: Aleksey V
authors.initials: AV
authors.lastname: Tolmachev
authors.forename: Yulei
authors.initials: Y
authors.lastname: Shen
authors.forename: Miao
authors.initials: M
authors.lastname: Liu
authors.forename: Lin
authors.initials: L
authors.lastname: Huang
authors.forename: Zhixin
authors.initials: Z
authors.lastname: Zhang
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Wing C
authors.initials: WC
authors.lastname: Chan
authors.forename: Steven H
authors.initials: SH
authors.lastname: Hinrichs
authors.forename: Kai
authors.initials: K
authors.lastname: Fu
authors.forename: Shi-Jian
authors.initials: SJ
authors.lastname: Ding
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid / Q000379:methods; D006801:Humans; D007553:Isotope Labeling / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000235:genetics; D011506:Proteins / Q000032:analysis* / Q000235:genetics; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins; D020543:Proteome