title: A paired ions scoring algorithm based on Morpheus for simultaneous identification and quantification of proteome samples prepared by isobaric peptide termini labeling strategies.
abstract: The isobaric peptide termini labeling (IPTL) method is a promising strategy in quantitative proteomics for its high accuracy, while the increased complexity of MS2 spectra originated from the paired b, y ions has adverse effect on the identification and the coverage of quantification. Here, a paired ions scoring algorithm (PISA) based on Morpheus, a database searching algorithm specifically designed for high-resolution MS2 spectra, was proposed to address this issue. PISA was first tested on two 1:1 mixed IPTL datasets, and increases in peptide to spectrum matchings, distinct peptides and protein groups compared to Morpheus itself and MASCOT were shown. Furthermore, the quantification is simultaneously performed and 100% quantification coverage is achieved by PISA since each of the identified peptide to spectrum matchings has several pairs of fragment ions which could be used for quantification. Then the PISA was applied to the relative quantification of human hepatocellular carcinoma cell lines with high and low metastatic potentials prepared by an IPTL strategy.
authors: Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors: Shen
authors: S
authors: Zhang
authors: Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors: Qi
authors: Q
authors: Wu
authors: Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.
authors: Yichu
authors: Y
authors: Shan
authors: Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.
authors: Zhigang
authors: Z
authors: Sui
authors: Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.
authors: Lihua
authors: L
authors: Zhang
authors: Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.
authors: Yukui
authors: Y
authors: Zhang
mesh_terms: D000465:Algorithms; D006528:Carcinoma, Hepatocellular / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D016208:Databases, Factual; D006367:HeLa Cells; D006801:Humans; D007553:Isotope Labeling; D008113:Liver Neoplasms / Q000378:metabolism / Q000473:pathology; D010455:Peptides / Q000737:chemistry*; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods
chemical_list: D010455:Peptides; D020543:Proteome
keywords: Bioinformatics; Database search algorithm; Isobaric peptide termini labeling; Morpheus; Paired ions scoring algorithm; Quantification