ppmFixer：用于 pGlyco3.0 的质量误差调整，以纠正近等压错配。

IF 3.4 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Glycobiology Pub Date : 2024-04-10 DOI:10.1093/glycob/cwae006

Trevor M Adams, Peng Zhao, Rui Kong, Lance Wells

{"title":"ppmFixer：用于 pGlyco3.0 的质量误差调整，以纠正近等压错配。","authors":"Trevor M Adams, Peng Zhao, Rui Kong, Lance Wells","doi":"10.1093/glycob/cwae006","DOIUrl":null,"url":null,"abstract":"Modern glycoproteomics experiments require the use of search engines due to the generation of countless spectra. While these tools are valuable, manual validation of search engine results is often required for detailed analysis of glycopeptides as false-discovery rates are often not reliable for glycopeptide data. Near-isobaric mismatches are a common source of misidentifications for the popular glycopeptide-focused search engine pGlyco3.0, and in this technical note we share a strategy and script that improves the accuracy of the search utilizing two manually validated datasets of the glycoproteins CD16a and HIV-1 Env as proof-of-principle.","PeriodicalId":12766,"journal":{"name":"Glycobiology","volume":" ","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11005163/pdf/","citationCount":"0","resultStr":"{\"title\":\"ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches.\",\"authors\":\"Trevor M Adams, Peng Zhao, Rui Kong, Lance Wells\",\"doi\":\"10.1093/glycob/cwae006\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Modern glycoproteomics experiments require the use of search engines due to the generation of countless spectra. While these tools are valuable, manual validation of search engine results is often required for detailed analysis of glycopeptides as false-discovery rates are often not reliable for glycopeptide data. Near-isobaric mismatches are a common source of misidentifications for the popular glycopeptide-focused search engine pGlyco3.0, and in this technical note we share a strategy and script that improves the accuracy of the search utilizing two manually validated datasets of the glycoproteins CD16a and HIV-1 Env as proof-of-principle.\",\"PeriodicalId\":12766,\"journal\":{\"name\":\"Glycobiology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.4000,\"publicationDate\":\"2024-04-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11005163/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Glycobiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/glycob/cwae006\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Glycobiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/glycob/cwae006","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

现代糖蛋白组学实验需要使用搜索引擎，因为会产生无数的图谱。虽然这些工具很有价值，但要对糖肽进行详细分析，往往需要人工验证搜索引擎的结果，因为糖肽数据的错误发现率通常并不可靠。对于流行的以糖肽为重点的搜索引擎 pGlyco3.0，近等位错配是常见的错误识别来源，在本技术报告中，我们分享了一种策略和脚本，利用两个人工验证的糖蛋白 CD16a 和 HIV-1 Env 数据集作为原理验证，提高了搜索的准确性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches.

Modern glycoproteomics experiments require the use of search engines due to the generation of countless spectra. While these tools are valuable, manual validation of search engine results is often required for detailed analysis of glycopeptides as false-discovery rates are often not reliable for glycopeptide data. Near-isobaric mismatches are a common source of misidentifications for the popular glycopeptide-focused search engine pGlyco3.0, and in this technical note we share a strategy and script that improves the accuracy of the search utilizing two manually validated datasets of the glycoproteins CD16a and HIV-1 Env as proof-of-principle.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Glycobiology 生物-生化与分子生物学

CiteScore

7.50

自引率

4.70%

发文量

审稿时长

3 months

期刊介绍： Established as the leading journal in the field, Glycobiology provides a unique forum dedicated to research into the biological functions of glycans, including glycoproteins, glycolipids, proteoglycans and free oligosaccharides, and on proteins that specifically interact with glycans (including lectins, glycosyltransferases, and glycosidases). Glycobiology is essential reading for researchers in biomedicine, basic science, and the biotechnology industries. By providing a single forum, the journal aims to improve communication between glycobiologists working in different disciplines and to increase the overall visibility of the field.