title: CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets.
abstract: The Chromosome-centric Human Proteome Project (C-HPP) aims to catalog genome-encoded proteins using a chromosome-by-chromosome strategy. As the C-HPP proceeds, the increasing requirement for data-intensive analysis of the MS/MS data poses a challenge to the proteomic community, especially small laboratories lacking computational infrastructure. To address this challenge, we have updated the previous CAPER browser into a higher version, CAPER 3.0, which is a scalable cloud-based system for data-intensive analysis of C-HPP data sets. CAPER 3.0 uses cloud computing technology to facilitate MS/MS-based peptide identification. In particular, it can use both public and private cloud, facilitating the analysis of C-HPP data sets. CAPER 3.0 provides a graphical user interface (GUI) to help users transfer data, configure jobs, track progress, and visualize the results comprehensively. These features enable users without programming expertise to easily conduct data-intensive analysis using CAPER 3.0. Here, we illustrate the usage of CAPER 3.0 with four specific mass spectral data-intensive problems: detecting novel peptides, identifying single amino acid variants (SAVs) derived from known missense mutations, identifying sample-specific SAVs, and identifying exon-skipping events. CAPER 3.0 is available at http://prodigy.bprc.ac.cn/caper3.
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Shuai
authors: S
authors: Yang
authors: Beijing Genestone Technology Ltd. , Beijing 100085, China.
authors: Xinlei
authors: X
authors: Zhang
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Lihong
authors: L
authors: Diao
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.|Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College , Beijing 100005, China.
authors: Feifei
authors: F
authors: Guo
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Dan
authors: D
authors: Wang
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Zhongyang
authors: Z
authors: Liu
authors: Beijing Genestone Technology Ltd. , Beijing 100085, China.
authors: Honglei
authors: H
authors: Li
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Junjie
authors: J
authors: Zheng
authors: Shandong Computer Science Center (National Supercomputer Center in Jinan) , Shandong 250101, China.
authors: Jingshan
authors: J
authors: Pan
authors: Department of Biochemistry and Molecular Biology, Monash University , Clayton, Victoria 3800, Australia.
authors: Edouard C
authors: EC
authors: Nice
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Dong
authors: D
authors: Li
authors: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.|National Center for Protein Sciences Beijing , Beijing 102206, China.
authors: Fuchu
authors: F
authors: He
mesh_terms: D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D000067917:Cloud Computing; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D020543:Proteome
chemical_list: D011506:Proteins; D020543:Proteome
keywords: Chromosome-centric Human Proteome Project; Proteomic data analysis platform; big data; bioinformatics; cloud computing; proteomic data visualization