{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T00:13:44Z","timestamp":1776471224867,"version":"3.51.2"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0siqiliu@genomics.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu397","type":"journal-article","created":{"date-parts":[[2014,7,23]],"date-time":"2014-07-23T06:44:50Z","timestamp":1406097890000},"page":"3136-3138","source":"Crossref","is-referenced-by-count":29,"title":["sapFinder: an R\/Bioconductor package for detection of variant peptides in shotgun proteomics experiments"],"prefix":"10.1093","volume":"30","author":[{"given":"Bo","family":"Wen","sequence":"first","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaohang","family":"Xu","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gloria M.","family":"Sheynkman","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiang","family":"Feng","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"},{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Lin","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quanhui","family":"Wang","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"},{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xun","family":"Xu","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"},{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"},{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"},{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siqi","family":"Liu","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"},{"name":"1 BGI-Shenzhen, Shenzhen 518083, China, 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, 3 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, 5 Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and 6 Macau University of Science and Technology, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,7,22]]},"reference":[{"key":"2023012711574890900_btu397-B1","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The SWISS-PROT 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