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

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 labo...

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Bibliographic Details
Published in:Journal of proteome research 2015-09, Vol.14 (9), p.3720-3728
Main Authors: Yang, Shuai, Zhang, Xinlei, Diao, Lihong, Guo, Feifei, Wang, Dan, Liu, Zhongyang, Li, Honglei, Zheng, Junjie, Pan, Jingshan, Nice, Edouard C, Li, Dong, He, Fuchu
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Chromosome Mapping
Cloud Computing
Databases, Protein
Humans
Molecular Sequence Data
Polymorphism, Genetic
Proteins - chemistry
Proteins - genetics
Proteome
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Summary: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.
ISSN:1535-3893
1535-3907
DOI:10.1021/pr501335w