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Wen B, Xu S, Zhou R, Zhang B, Wang X, Liu X, Xu X, Liu S. PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. BMC Bioinformatics 2016; 17:244. [PMID: 27316337 PMCID: PMC4912784 DOI: 10.1186/s12859-016-1133-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 06/09/2016] [Indexed: 11/27/2022] Open
Abstract
Background Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database. Obviously, this strategy could not identify peptide and protein sequences that are absent from a reference database. A customized protein database on the basis of RNA-Seq data is thus proposed to assist with and improve the identification of novel peptides. Correspondingly, development of a comprehensive pipeline, which provides an end-to-end solution for novel peptide detection with the customized protein database, is necessary. Results A pipeline with an R package, assigned as a PGA utility, was developed that enables automated treatment to the tandem mass spectrometry (MS/MS) data acquired from different MS platforms and construction of customized protein databases based on RNA-Seq data with or without a reference genome guide. Hence, PGA can identify novel peptides and generate an HTML-based report with a visualized interface. On the basis of a published dataset, PGA was employed to identify peptides, resulting in 636 novel peptides, including 510 single amino acid polymorphism (SAP) peptides, 2 INDEL peptides, 49 splice junction peptides, and 75 novel transcript-derived peptides. The software is freely available from http://bioconductor.org/packages/PGA/, and the example reports are available at http://wenbostar.github.io/PGA/. Conclusions The pipeline of PGA, aimed at being platform-independent and easy-to-use, was successfully developed and shown to be capable of identifying novel peptides by searching the customized protein database derived from RNA-Seq data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1133-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bo Wen
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Ruo Zhou
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Bing Zhang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Xiaojing Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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Huang PJ, Lee CC, Tan BCM, Yeh YM, Julie Chu L, Chen TW, Chang KP, Lee CY, Gan RC, Liu H, Tang P. CMPD: cancer mutant proteome database. Nucleic Acids Res 2014; 43:D849-55. [PMID: 25398898 PMCID: PMC4383976 DOI: 10.1093/nar/gku1182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Whole-exome sequencing, which centres on the protein coding regions of disease/cancer associated genes, represents the most cost-effective method to-date for deciphering the association between genetic alterations and diseases. Large-scale whole exome/genome sequencing projects have been launched by various institutions, such as NCI, Broad Institute and TCGA, to provide a comprehensive catalogue of coding variants in diverse tissue samples and cell lines. Further functional and clinical interrogation of these sequence variations must rely on extensive cross-platforms integration of sequencing information and a proteome database that explicitly and comprehensively archives the corresponding mutated peptide sequences. While such data resource is a critical for the mass spectrometry-based proteomic analysis of exomic variants, no database is currently available for the collection of mutant protein sequences that correspond to recent large-scale genomic data. To address this issue and serve as bridge to integrate genomic and proteomics datasets, CMPD (http://cgbc.cgu.edu.tw/cmpd) collected over 2 millions genetic alterations, which not only facilitates the confirmation and examination of potential cancer biomarkers but also provides an invaluable resource for translational medicine research and opportunities to identify mutated proteins encoded by mutated genes.
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Affiliation(s)
- Po-Jung Huang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Chi-Ching Lee
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | | | - Yuan-Ming Yeh
- Bioinformatics Division, Tri-I Biotech, Inc., Taipei 221, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Ting-Wen Chen
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Lin-Kou, Taoyuan 333, Taiwan
| | - Cheng-Yang Lee
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | - Ruei-Chi Gan
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | - Hsuan Liu
- Department of Molecular and Cellular Biology, Chang Gung University, Taoyuan 333, Taiwan
| | - Petrus Tang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
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Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S. sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. ACTA ACUST UNITED AC 2014; 30:3136-8. [PMID: 25053745 DOI: 10.1093/bioinformatics/btu397] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
UNLABELLED Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface. AVAILABILITY AND IMPLEMENTATION sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license.
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Affiliation(s)
- Bo Wen
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Shaohang Xu
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Gloria M Sheynkman
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Qiang Feng
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Liang Lin
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Quanhui Wang
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, Ch
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China
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