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

Type Information
Nr 48 (Research article)
Authors Röst, Hannes; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars
Title Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.
Journal Bioinformatics (2015) 31(14) 2415-7
DOI 10.1093/bioinformatics/btv152
Citations 9 citations (journal impact: 4.62)
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 httpscode.google.compmsproteomicstools.
Synopsis We describe software that can be used to visualize results from targeted proteomics studies.