Journal
JOURNAL OF PROTEOME RESEARCH
Volume 14, Issue 9, Pages 3720-3728Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr501335w
Keywords
Proteomic data analysis platform; proteomic data visualization; bioinformatics; cloud computing; big data; Chromosome-centric Human Proteome Project
Categories
Funding
- Chinese Program of International ST Cooperation [2014DFB30020]
- Chinese High Technology Research and Development [2015AA020108, 2012AA020201]
- National Natural Science Foundation of China [31271407]
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The Chromosome-centric Human Proteome Project (CHPP) 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 CHPP 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.
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