{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T02:42:31Z","timestamp":1761100951903},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":3299,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Integrating qualitative protein identification with quantitative protein analysis is non-trivial, given incompatibility in output formats. We present TandTRAQ, a standalone utility that integrates results from i-Tracker, an open-source iTRAQ quantitation program with the search results from X?Tandem, an open-source proteome search engine. The utility runs from the command-line and can be easily integrated into a pipeline for automation.<\/jats:p><jats:p>Availability: The TandTRAQ Perl scripts are freely available for download at http:\/\/www.ohsucancer.com\/isrdev\/tandtraq\/<\/jats:p><jats:p>Contact: \u00a0laderast@ohsu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm467","type":"journal-article","created":{"date-parts":[[2007,9,26]],"date-time":"2007-09-26T02:14:39Z","timestamp":1190772879000},"page":"3394-3396","source":"Crossref","is-referenced-by-count":12,"title":["<i>TandTRAQ<\/i>: an open-source tool for integrated protein identification and quantitation"],"prefix":"10.1093","volume":"23","author":[{"given":"Ted","family":"Laderas","sequence":"first","affiliation":[{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"},{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cory","family":"Bystrom","sequence":"additional","affiliation":[{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debra","family":"McMillen","sequence":"additional","affiliation":[{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guang","family":"Fan","sequence":"additional","affiliation":[{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shannon","family":"McWeeney","sequence":"additional","affiliation":[{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"},{"name":"1 Informatics Shared Resource, OHSU Cancer Institute, 2Oregon Clinical and Translational Research Institute, 3Proteomics Shared Resource and 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon 97212, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,9,25]]},"reference":[{"key":"2023041107434913300_","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":"2023041107434913300_","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"TANDEM: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041107434913300_","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/bioinformatics\/15.4.339","article-title":"The biopolymer markup language","volume":"15","author":"Fenyo","year":"1999","journal-title":"Bioinformatics"},{"key":"2023041107434913300_","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/13690","article-title":"Quantitative analysis of complex protein mixtures using isotope-coded affinity tags","volume":"17","author":"Gygi","year":"1999","journal-title":"Nat. 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