ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches
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 reliabl...
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| Veröffentlicht in: | Glycobiology (Oxford) 2024-04, Vol.34 (4) |
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| container_title | Glycobiology (Oxford) |
| container_volume | 34 |
| creator | Adams, Trevor M Zhao, Peng Kong, Rui Wells, Lance |
| description | 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. |
| doi_str_mv | 10.1093/glycob/cwae006 |
| format | Article |
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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.</description><identifier>ISSN: 1460-2423</identifier><identifier>EISSN: 1460-2423</identifier><identifier>DOI: 10.1093/glycob/cwae006</identifier><identifier>PMID: 38263491</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Glycopeptides ; Glycosylation ; Proteomics - methods ; Search Engine ; Tandem Mass Spectrometry</subject><ispartof>Glycobiology (Oxford), 2024-04, Vol.34 (4)</ispartof><rights>The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2024</rights><rights>The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c284t-72fb8b49714cad83bd780000a9cbc90fb6f21f25e19754d0011bb8f2b0c22a863</cites><orcidid>0000-0003-4956-5363 ; 0000-0002-9296-5293</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,1578,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38263491$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Adams, Trevor M</creatorcontrib><creatorcontrib>Zhao, Peng</creatorcontrib><creatorcontrib>Kong, Rui</creatorcontrib><creatorcontrib>Wells, Lance</creatorcontrib><title>ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches</title><title>Glycobiology (Oxford)</title><addtitle>Glycobiology</addtitle><description>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.</description><subject>Glycopeptides</subject><subject>Glycosylation</subject><subject>Proteomics - methods</subject><subject>Search Engine</subject><subject>Tandem Mass Spectrometry</subject><issn>1460-2423</issn><issn>1460-2423</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkDFPwzAQhS0EoqWwMiKPMKT12Wlis6GKFqRKDMAc2Y4NqZI62I6g_55UKYiNW-5O-u7d00PoEsgUiGCzt3qnnZrpT2kIyY7QGNKMJDSl7PjPPEJnIWwIgQz4_BSNGKcZSwWM0XPbNsvqy_hbLHEjQ8DGe-exLDddiI3ZRmz7tV3t_7ApwdFh7bw3OuKtkT6pglPSVxo3VWhk1O8mnKMTK-tgLg59gl6X9y-Lh2T9tHpc3K0TTXkak5xaxVUqcki1LDlTZc5JX1JopQWxKrMULJ0bEPk8LXv3oBS3VBFNqeQZm6DrQbf17qMzIRa9B23qWm6N60JBBXAQggH06HRAtXcheGOL1leN9LsCSLEPshiCLA5B9gdXB-1ONab8xX-S64GbAXBd-5_YN57nfxU</recordid><startdate>20240410</startdate><enddate>20240410</enddate><creator>Adams, Trevor M</creator><creator>Zhao, Peng</creator><creator>Kong, Rui</creator><creator>Wells, Lance</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-4956-5363</orcidid><orcidid>https://orcid.org/0000-0002-9296-5293</orcidid></search><sort><creationdate>20240410</creationdate><title>ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches</title><author>Adams, Trevor M ; Zhao, Peng ; Kong, Rui ; Wells, Lance</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c284t-72fb8b49714cad83bd780000a9cbc90fb6f21f25e19754d0011bb8f2b0c22a863</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Glycopeptides</topic><topic>Glycosylation</topic><topic>Proteomics - methods</topic><topic>Search Engine</topic><topic>Tandem Mass Spectrometry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Adams, Trevor M</creatorcontrib><creatorcontrib>Zhao, Peng</creatorcontrib><creatorcontrib>Kong, Rui</creatorcontrib><creatorcontrib>Wells, Lance</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Glycobiology (Oxford)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Adams, Trevor M</au><au>Zhao, Peng</au><au>Kong, Rui</au><au>Wells, Lance</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches</atitle><jtitle>Glycobiology (Oxford)</jtitle><addtitle>Glycobiology</addtitle><date>2024-04-10</date><risdate>2024</risdate><volume>34</volume><issue>4</issue><issn>1460-2423</issn><eissn>1460-2423</eissn><abstract>Abstract
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| language | eng |
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| source | MEDLINE; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Glycopeptides Glycosylation Proteomics - methods Search Engine Tandem Mass Spectrometry |
| title | ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches |
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