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  • Title: STEM: a software tool for large-scale proteomic data analyses.
    Author: Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T.
    Journal: J Proteome Res; 2005; 4(5):1826-31. PubMed ID: 16212438.
    Abstract:
    We describe the software, STEM (STrategic Extractor for Mascot's results), which efficiently processes large-scale mass spectrometry-based proteomics data. V (View)-mode evaluates the Mascot peptide identification dataset, removes unreliable candidates and redundant assignments, and integrates the results with key information in the experiment. C (Comparison)-mode compares peptide coverage among multiple datasets and displays proteins commonly/specifically found therein, and processes data for quantitative studies that utilize conventional isotope tags or tags having a smaller mass difference. STEM significantly improves throughput of proteomics study.
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