Article pubs.acs.org/jpr
CAPER: a Chromosome-Assembled human Proteome browsER Feifei Guo,†,‡,# Dan Wang,‡,# Zhongyang Liu,‡,# Liang Lu,‡ Wei Zhang,‡,§ Haiyan Sun,‡,∥ Hongxing Zhang,‡ Jie Ma,‡ Songfeng Wu,‡ Ning Li,‡ Ying Jiang,‡ Weimin Zhu,‡ Jun Qin,‡ Ping Xu,*,‡ Dong Li,*,‡ and Fuchu He*,†,‡ †
Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100005, China ‡ State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China § Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, 410073, China ∥ Department of Stomatology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing, 100071, China ABSTRACT: High-throughput mass spectrometry and antibody-based experiments have begun to produce a large amount of proteomic data sets. Chromosome-based visualization of these data sets and their annotations can help effectively integrate, organize, and analyze them. Therefore, we developed a web-based, user-friendly ChromosomeAssembled human Proteome browsER (CAPER). To display proteomic data sets and related annotations comprehensively, CAPER employs two distinct visualization strategies: track-view for the sequence/site information and the correspondence between proteome, transcriptome, genome, and chromosome and heatmap-view for the qualitative and quantitative functional annotations. CAPER supports data browsing at multiple scales through Google Map-like smooth navigation, zooming, and positioning with chromosomes as the reference coordinate. Both track-view and heatmap-view can mutually switch, providing a high-quality user interface. Taken together, CAPER will greatly facilitate the complete annotation and functional interpretation of the human genome by proteomic approaches, thereby making a significant contribution to the Chromosome-Centric Human Proteome Project and even the human physiology/pathology research. CAPER can be accessed at http://www.bprc.ac.cn/CAPE. KEYWORDS: proteomic data, chromosome-centric visualization, proteome browser, human genome annotation, bioinformatics, Chromosome-Centric Human Proteome Project
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INTRODUCTION In the post-genomic era, it is an important task to annotate the human genome after the complete sequencing, to provide the resource for human physiology and pathology studies. Expressed sequence tags (EST) and full coding DNAs (cDNA) have been widely used to identify the protein coding genes.1,2 With the development of biological technologies, proteomic approaches have begun to play important roles in genome annotation. On one hand, mapping the identified peptides from mass spectrometry (MS) to the genome provides direct translation-level evidence for protein coding regions in genome, contributing to the confirmation and correction of existing gene models, even the discovery of novel protein coding genes.2 On the other hand, protein identification by proteomic methods helps us characterize the expression states of gene products in different disease states, tissues, and stages of development, contributing to functional interpretation of the human genome.1 High-throughput proteomic experiments have generated large amounts of peptide identification data sets, which have © 2012 American Chemical Society
been stored and disseminated by multiple databases, such as PeptideAtlas,3 Human Proteinpedia,4 PRIDE,5 and GPMDB.6 In 2010, the Chromosome-Centric Human Proteome Project (C-HPP) was launched, the initial goal of which is to use sensitive mass spectrometry and antibody reagents to identify at least one representative protein encoded by each of the approximately 20,300 genes on human chromosomes, simultaneously obtaining various kinds of annotation information including tissue localization, post-translational modification (PTM), and so on.7 To promote mapping and annotating the full set of human proteome by international efforts, C-HPP takes a “chromosome-by-chromosome” strategy.7 As of September, 2012, all 24 chromosomes have been claimed by international teams. As C-HPP proceeds, more and more proteomic data sets will be produced in the foreseeable future. Special Issue: Chromosome-centric Human Proteome Project Received: August 31, 2012 Published: December 20, 2012 179
dx.doi.org/10.1021/pr300831z | J. Proteome Res. 2013, 12, 179−186
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