ArticleBioinformatics (Oxford, England)2014
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
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Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18citing papers in PubMed
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18 citing papers in PubMed.
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- ProteoformDB: A Built-In Application to Generate Proteoform Database.Journal of proteome research · 2026Article
- Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025Article
- Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants.Proteomes · 2024Article
- Chemoproteogenomic stratification of the missense variant cysteinome.Nature communications · 2024Article
- Multi-omic stratification of the missense variant cysteinome.bioRxiv : the preprint server for biology · 2023Article
- A-to-I nonsynonymous RNA editing was significantly enriched in the ubiquitination site and correlated with clinical features and immune response.Scientific reports · 2022Article
- REIA: A database for cancer A-to-I RNA editing with interactive analysis.International journal of biological sciences · 2022Article
- Article
- RNA editing derived epitopes function as cancer antigens to elicit immune responses.Nature communications · 2018Article
- A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer.Cancer cell · 2018Article
- Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys.BMC genomics · 2017Article
- Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify.Molecular & cellular proteomics : MCP · 2017Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Improvement of peptide identification with considering the abundance of mRNA and peptide.BMC bioinformatics · 2017Article
- Large scale analysis of amino acid substitutions in bacterial proteomics.BMC bioinformatics · 2016Article
- PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.BMC bioinformatics · 2016Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
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Authors and funding
9 authors.
Bo WenBGI-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 XuBGI-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 SheynkmanBGI-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 FengBGI-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 LinBGI-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 WangBGI-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 XuBGI-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 WangBGI-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 LiuBGI-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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledSingle 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.
Indexed as
Amino Acid SubstitutionSoftwareGenetic VariationHigh-Throughput Nucleotide SequencingPeptidesProteomicsTandem Mass SpectrometryPeptides
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