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STEM: a software tool for large-scale proteomic data analyses.

Takashi Shinkawa·Masato Taoka·Yoshio Yamauchi·Tohru Ichimura·Hiroyuki Kaji·Nobuhiro Takahashi·Toshiaki Isobe
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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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AlgorithmsAmino Acid SequenceAnimalsBacterial ProteinsChromatography, LiquidComputational BiologyDatabases, ProteinElectrophoresis, Gel, Two-DimensionalHumansMass SpectrometryModels, StatisticalMolecular Sequence DataPeptide MappingPeptidesProteomeProteomicsSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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Takashi Shinkawa, Masato Taoka, Yoshio Yamauchi, Tohru Ichimura, Hiroyuki Kaji, Nobuhiro Takahashi, Toshiaki Isobe. STEM: a software tool for large-scale proteomic data analyses.. https://doi.org/10.1021/pr050167x

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