{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T12:15:35Z","timestamp":1763468135711},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Sipros\/ProRata is an open-source software package for end-to-end data analysis in a wide variety of community proteomics measurements. A database-searching program, Sipros 3.0, was developed for accurate general-purpose protein identification and broad-range post-translational modification searches. Hybrid Message Passing Interface\/OpenMP parallelism of the new Sipros architecture allowed its computation to be scalable from desktops to supercomputers. The upgraded ProRata 3.0 performs label-free quantification and isobaric chemical labeling quantification in addition to metabolic labeling quantification. Sipros\/ProRata is a versatile informatics system that enables identification and quantification of proteins and their variants in many types of community proteomics studies.<\/jats:p>\n               <jats:p>Availability: Both programs are freely available under the GNU GPL license at Sipros.omicsbio.org and ProRata.omicsbio.org.<\/jats:p>\n               <jats:p>Contact: \u00a0panc@ornl.gov<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt329","type":"journal-article","created":{"date-parts":[[2013,6,23]],"date-time":"2013-06-23T00:20:14Z","timestamp":1371946814000},"page":"2064-2065","source":"Crossref","is-referenced-by-count":31,"title":["Sipros\/ProRata: a versatile informatics system for quantitative community proteomics"],"prefix":"10.1093","volume":"29","author":[{"given":"Yingfeng","family":"Wang","sequence":"first","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory and 2Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tae-Hyuk","family":"Ahn","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory and 2Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhou","family":"Li","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory and 2Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chongle","family":"Pan","sequence":"additional","affiliation":[{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory and 2Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA"},{"name":"1 Computer Science and Mathematics Division, Oak Ridge National Laboratory and 2Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,6,21]]},"reference":[{"key":"2023020305302345400_btt329-B1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.febslet.2004.07.055","article-title":"Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments","volume":"573","author":"Breitling","year":"2004","journal-title":"FEBS Lett."},{"key":"2023020305302345400_btt329-B2","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","article-title":"An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database","volume":"5","author":"Eng","year":"1994","journal-title":"J. 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