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J Proteome Res. 2015 Sep 4;14(9):3720-8. doi: 10.1021/pr501335w. Epub 2015 Mar 27.

CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets.

Yang S1,2, Zhang X3, Diao L1,2, Guo F1,2,4, Wang D1,2, Liu Z1,2, Li H3, Zheng J1,2, Pan J5, Nice EC6, Li D1,2, He F1,2.

Author information

1
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100850, China.
2
National Center for Protein Sciences Beijing , Beijing 102206, China.
3
Beijing Genestone Technology Ltd. , Beijing 100085, China.
4
Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College , Beijing 100005, China.
5
Shandong Computer Science Center (National Supercomputer Center in Jinan) , Shandong 250101, China.
6
Department of Biochemistry and Molecular Biology, Monash University , Clayton, Victoria 3800, Australia.

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.

KEYWORDS:

Chromosome-centric Human Proteome Project; Proteomic data analysis platform; big data; bioinformatics; cloud computing; proteomic data visualization

PMID:
25794139
DOI:
10.1021/pr501335w
[Indexed for MEDLINE]

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