title: Sipros/ProRata: a versatile informatics system for quantitative community proteomics.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  Both programs are freely available under the GNU GPL license at Sipros.omicsbio.org and ProRata.omicsbio.org.
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Yingfeng
authors.initials: Y
authors.lastname: Wang
authors.forename: Tae-Hyuk
authors.initials: TH
authors.lastname: Ahn
authors.forename: Zhou
authors.initials: Z
authors.lastname: Li
authors.forename: Chongle
authors.initials: C
authors.lastname: Pan
mesh_terms: D030562:Databases, Protein; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D011506:Proteins