UNiquant, a program for quantitative proteomics analysis using stable isotope labeling

Xin Huang, Aleksey V. Tolmachev, Yulei Shen, Miao Liu, Lin Huang, Zhixin Zhang, Gordon A. Anderson, Richard D. Smith, Wing C. Chan, Steven H. Hinrichs, Kai Fu, Shi Jian Ding

Research output: Contribution to journalArticle

16 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1228-1237
Number of pages10
JournalJournal of proteome research
Volume10
Issue number3
DOIs
StatePublished - Mar 4 2011

Keywords

  • LC-MS/MS
  • Quantitative proteomics
  • Software Development
  • Stable isotope labeling

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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  • Cite this

    Huang, X., Tolmachev, A. V., Shen, Y., Liu, M., Huang, L., Zhang, Z., Anderson, G. A., Smith, R. D., Chan, W. C., Hinrichs, S. H., Fu, K., & Ding, S. J. (2011). UNiquant, a program for quantitative proteomics analysis using stable isotope labeling. Journal of proteome research, 10(3), 1228-1237. https://doi.org/10.1021/pr1010058