Improved quantitative analysis of mass spectrometry using quadratic equations

Joo Young Yoon, Kyung Young Lim, Sunho Lee, Kunsoo Park, Eunok Paek, Un Beom Kang, Jeonghun Yeom, Cheolju Lee

Research output: Contribution to journalArticle

10 Scopus citations


Protein quantification is one of the principal computational problems in mass spectrometry (MS) based proteomics. For robust and trustworthy protein quantification, accurate peptide quantification must be preceded. In recent years, stable isotope labeling has become the most popular method for relative quantification of peptides. However, some stable isotope labeling methods may carry a critical problem, which is an overlap of isotopic clusters. If the mass difference between the light- and heavy-labeled peptides is very small, the overlap of their isotopic clusters becomes larger as the mass of original peptide increases. Here we propose a new algorithm for peptide quantification that separates overlapping isotopic clusters using quadratic equations. It can be easily applied in Trans-Proteomic Pipeline (TPP) instead of XPRESS. For the mTRAQ-labeled peptides obtained by an Orbitrap mass spectrometer, it showed more accurate ratios and better standard deviations than XPRESS. Especially, for the peptides that do not contain lysine, the ratio difference between XPRESS and our algorithm became larger as the peptide masses increased. We expect that this algorithm can also be applied to other labeling methods such as 18O labeling and acrylamide labeling.

Original languageEnglish
Pages (from-to)2775-2785
Number of pages11
JournalJournal of Proteome Research
Issue number5
StatePublished - 2010 May 7


  • MTRAQ labeling
  • Mass spectrometry
  • Peptide quantification
  • Quadratic equation
  • Stable isotope labeling

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    Yoon, J. Y., Lim, K. Y., Lee, S., Park, K., Paek, E., Kang, U. B., Yeom, J., & Lee, C. (2010). Improved quantitative analysis of mass spectrometry using quadratic equations. Journal of Proteome Research, 9(5), 2775-2785.