{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T18:25:06Z","timestamp":1778869506094,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and implementation: TAPIR is available for all computing platforms under the 3-clause BSD license at https:\/\/github.com\/msproteomicstools\/msproteomicstools.<\/jats:p>\n               <jats:p>Contact: \u00a0lars@imsb.biol.ethz.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv152","type":"journal-article","created":{"date-parts":[[2015,3,19]],"date-time":"2015-03-19T01:13:52Z","timestamp":1426727632000},"page":"2415-2417","source":"Crossref","is-referenced-by-count":15,"title":["Efficient visualization of high-throughput targeted proteomics experiments: TAPIR"],"prefix":"10.1093","volume":"31","author":[{"given":"Hannes L.","family":"R\u00f6st","sequence":"first","affiliation":[{"name":"1 ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and"},{"name":"2 Ph.D. Program in Systems Biology, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Rosenberger","sequence":"additional","affiliation":[{"name":"1 ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and"},{"name":"2 Ph.D. Program in Systems Biology, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruedi","family":"Aebersold","sequence":"additional","affiliation":[{"name":"1 ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lars","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 ETH Zurich, Institute of Molecular Systems Biology, CH-8093 Zurich, Switzerland and"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,3,18]]},"reference":[{"key":"2023020202153394200_btv152-B1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based proteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"key":"2023020202153394200_btv152-B2","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1093\/bioinformatics\/bts066","article-title":"pymzML\u2013python module for high-throughput bioinformatics on mass spectrometry data","volume":"28","author":"Bald","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020202153394200_btv152-B3","doi-asserted-by":"crossref","first-page":"R111.015040","DOI":"10.1074\/mcp.R111.015040","article-title":"TraML\u2013a standard format for exchange of selected reaction monitoring transition lists","volume":"11","author":"Deutsch","year":"2012","journal-title":"Mol. 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