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Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

Citation Rost, Hannes; Rosenberger, George; Aebersold, Ruedi; Malmstrom, Lars; Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (2015), 0: -.
Abstract MOTIVATION: Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. RESULTS: We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. AVAILABILITY: TAPIR is available for all computing platforms under the 3-clause BSD license at https://code.google.com/p/msproteomicstools.
Synopsis We describe software that can be used to visualize results from targeted proteomics studies.
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