title: Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.
abstract: BACKGROUND
  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.
  
  
  METHODS
  TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools.
authors: ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and Ph.D. Program in Systems Biology, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland.
authors: Hannes L
authors: HL
authors: Röst
authors: ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and Ph.D. Program in Systems Biology, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland.
authors: George
authors: G
authors: Rosenberger
authors: ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and.
authors: Ruedi
authors: R
authors: Aebersold
authors: ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and.
authors: Lars
authors: L
authors: Malmström
mesh_terms: D003196:Computer Graphics; D013058:Mass Spectrometry; D040901:Proteomics / Q000379:methods*; D012984:Software