Multi-Q: A Fully Automated Tool for Multiplexed Protein Quantitation

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• 作者：Wen-Ting Lin ; Wei-Neng Hung ; Yi-Hwa Yian ; Kun-Pin Wu ; Chia-Li Han ; Yet-Ran Chen ; Yu-Ju Chen ; Ting-Yi Sung ; Wen-Lian Hsu
• 刊名：Journal of Proteome Research
• 出版年：2006
• 出版时间：September 2006
• 年：2006
• 卷：5
• 期：9
• 页码：2328 - 2338
• 全文大小：313K
• 年卷期：v.5,no.9(September 2006)
• ISSN：1535-3907

文摘

The iTRAQ labeling method combined with shotgun proteomic techniques represents a new dimensionin multiplexed quantitation for relative protein expression measurement in different cell states. Toexpedite the analysis of vast amounts of spectral data, we present a fully automated software package,called Multi-Q, for multiplexed iTRAQ-based quantitation in protein profiling. Multi-Q is designed as ageneric platform that can accommodate various input data formats from search engines and massspectrometer manufacturers. To calculate peptide ratios, the software automatically processes iTRAQ'ssignature peaks, including peak detection, background subtraction, isotope correction, and normalizationto remove systematic errors. Furthermore, Multi-Q allows users to define their own data-filteringthresholds based on semiempirical values or statistical models so that the computed results of foldchanges in peptide ratios are statistically significant. This feature facilitates the use of Multi-Q withvarious instrument types with different dynamic ranges, which is an important aspect of iTRAQ analysis.The performance of Multi-Q is evaluated with a mixture of 10 standard proteins and human Jurkat Tcells. The results are consistent with expected protein ratios and thus demonstrate the high accuracy,full automation, and high-throughput capability of Multi-Q as a large-scale quantitation proteomicstool. These features allow rapid interpretation of output from large proteomic datasets without theneed for manual validation. Executable Multi-Q files are available on Windows platform at http://ms.iis.sinica.edu.tw/Multi-Q/.