CAPER 2.0: An Interactive, Configurable, and Extensible Workflow- Based Platform to Analyze Data Sets from the Chromosome-centric Human Proteome Project Dan Wang, †,‡,§,# Zhongyang Liu, †,‡,§,# Feifei Guo, †,‡,§,∥,# Lihong Diao, †,‡,§ Yang Li, †,‡,§ Xinlei Zhang, ⊥ Zechi Huang, ⊥ Dong Li,* ,†,‡,§ and Fuchu He* ,†,‡,§,∥ † State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park Road, Beijing 100850, China ‡ National Center for Protein Sciences Beijing, 33 Life Science Park Road, Beijing 102206, China § National Engineering Research Center for Protein Drugs, 33 Life Science Park Road, Beijing 100850, China ∥ Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China ⊥ Beijing Genestone Technology, Ltd., F21-103, FengLinLvZhou, Kexueyuan Nanli, Datun Road, Beijing 100085, China ABSTRACT: The Chromosome-centric Human Proteome Project (C-HPP) aims to map and annotate the entire human proteome by the “chromosome-by-chromosome” strategy. As the C-HPP proceeds, the increasing volume of proteomic data sets presents a challenge for customized and reproducible bioinformatics data analyses for mining biological knowledge. To address this challenge, we updated the previous static proteome browser CAPER into a higher version, CAPER 2.0 − an interactive, configurable and extensible workflow- based platform for C-HPP data analyses. In addition to the previous visualization functions of track-view and heatmap- view, CAPER 2.0 presents a powerful toolbox for C-HPP data analyses and also integrates a configurable workflow system that supports the view, construction, edit, run, and share of workflows. These features allow users to easily conduct their own C-HPP proteomic data analyses and visualization by CAPER 2.0. We illustrate the usage of CAPER 2.0 with four specific workflows for finding missing proteins, mapping peptides to chromosomes for genome annotation, integrating peptides with transcription factor binding sites from ENCODE data sets, and functionally annotating proteins. The updated CAPER is available at http://www.bprc.ac.cn/CAPE. KEYWORDS: proteomic data analysis platform, user-customized workflow, proteomic data visualization, bioinformatics, Chromosome-centric Human Proteome Project ■ INTRODUCTION As an important component of the Human Proteome Project (HPP) established by the Human Proteome Organization (HUPO), the Chromosome-centric Human Proteome Project (C-HPP) was officially launched in Geneva in 2011. 1 The C- HPP aims to identify the entire human protein set encoded in each chromosome and to characterize them with abundance, tissue/subcellular localization, post-translational modification (PTM), single amino acid variant (SAAV) generated by nonsynonymous single nucleotide polymorphism (nsSNP), interactome, and so on. 2,3 To achieve these scientific objects, the C-HPP consortium takes a “chromosome-by-chromosome” international cooperation strategy. Now all 24 chromosomes and mitochondria have been “adopted” by 25 teams from the world, 1 and the research achievements of the first phase have been published in the 2013 C-HPP special issue of the Journal of Proteome Research. 4 In particular, the C-HPP consortium is strengthening the cooperation with the Encyclopedia of DNA Elements (ENCODE) Consortium, whose goal is to build a comprehensive parts list of functional elements in the human genome. 5 This cooperation between the two projects is promising to promote the elucidation of how the interacting genomic elements such as polygenes, SNPs, and transcription factors control the families of isoforms generated at the protein level. 6 As the C-HPP proceeds, large amounts of proteomic data sets have been produced. 4 It is challenging to extract biologically important information from these large-scale, Special Issue: Chromosome-centric Human Proteome Project Received: August 1, 2013 Published: November 22, 2013 Article pubs.acs.org/jpr © 2013 American Chemical Society 99 dx.doi.org/10.1021/pr400795c | J. Proteome Res. 2014, 13, 99−106