title: STEM: a software tool for large-scale proteomic data analyses.
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.
authors.affiliation: Integrated Proteomics System Project, Pioneer Research on Genome the Frontier, MEXT, c/o Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji-shi, Tokyo 192-0397, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Shinkawa
authors.forename: Masato
authors.initials: M
authors.lastname: Taoka
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Yamauchi
authors.forename: Tohru
authors.initials: T
authors.lastname: Ichimura
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kaji
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Takahashi
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Isobe
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D013058:Mass Spectrometry; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D001426:Bacterial Proteins; D010455:Peptides; D020543:Proteome