Yoon, Joo Young Lim, Kyung Young Lee, Sunho Park, Kunsoo Paek, Eunok Kane, Un-Beom Yeom, Jeonghun Lee, Cheolju 2024-01-20T19:31:45Z 2024-01-20T19:31:45Z 2021-09-02 2010-05 1535-3893 https://pubs.kist.re.kr/handle/201004/131526 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 O-18 labeling and acrylamide labeling. English AMER CHEMICAL SOC CODED AFFINITY TAGS PEPTIDE IDENTIFICATION PROTEIN IDENTIFICATION MONOISOTOPIC MASSES SEQUENCE DATABASES LABELED PEPTIDES SOFTWARE TOOL LC-MS PROTEOMICS QUANTIFICATION Improved Quantitative Analysis of Mass Spectrometry using Quadratic Equations Article 10.1021/pr100183t 1 JOURNAL OF PROTEOME RESEARCH, v.9, no.5, pp.2775 - 2785 JOURNAL OF PROTEOME RESEARCH 9 5 2775 2785 scie scopus 000277353200067 2-s2.0-77952079146 Biochemical Research Methods Biochemistry & Molecular Biology Article CODED AFFINITY TAGS PEPTIDE IDENTIFICATION PROTEIN IDENTIFICATION MONOISOTOPIC MASSES SEQUENCE DATABASES LABELED PEPTIDES SOFTWARE TOOL LC-MS PROTEOMICS QUANTIFICATION mass spectrometry peptide quantification mTRAQ labeling quadratic equation stable isotope labeling