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Analysis and Annotation of c-Type Ions in Peptide Mass Spectral Libraries.

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Τίτλος: Analysis and Annotation of c-Type Ions in Peptide Mass Spectral Libraries.
Συγγραφείς: Burke MC; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States., Yang X; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States., Liang Y; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States., Neta P; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States., Stein SE; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States.
Πηγή: Journal of proteome research [J Proteome Res] 2026 Aug 07; Vol. 25 (8), pp. 4315-4321.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE
Imprint Name(s): Original Publication: Washington, D.C. : American Chemical Society, c2002-
Ιατρικοί όροι (MeSH): Peptides*/chemistry , Peptides*/analysis , Proteomics*/methods , Peptide Library*, Ions/chemistry ; Tandem Mass Spectrometry/methods ; Humans ; Amino Acid Sequence
Περίληψη: The large collection of high-quality mass spectra in the NIST Human HCD Peptide and NIST Tandem Mass Spectral Libraries is used to understand the role of peptide sequence in c-type ion formation in beam-type collision-induced dissociation. Furthermore, results from the analyses were used to inform and apply annotation rules for c-type ions in the updated Human HCD Peptide Mass Spectral Library. As a result, 155,663 c-type ions are now annotated, providing additional peptide sequence information, often where b- and y-type ions may be lacking. Examples shown here highlight the significance of these c-type ions, both in terms of their relative abundance and in resolving peptide-sequence ambiguities. Furthermore, these examples illustrate the value of including c-type ions to improve searching and scoring of peptide spectrum matches.
(Not subject to U.S. Copyright. Published 2026 by American Chemical Society.)
References: J Am Soc Mass Spectrom. 1993 Nov;4(11):874-31. (PMID: 24227531)
J Proteome Res. 2012 Nov 2;11(11):5479-91. (PMID: 22998608)
J Am Soc Mass Spectrom. 2013 Aug;24(8):1228-41. (PMID: 23722727)
Rapid Commun Mass Spectrom. 2004;18(18):2069-76. (PMID: 15378720)
Mass Spectrom Rev. 2009 Jul-Aug;28(4):640-54. (PMID: 19338048)
J Am Soc Mass Spectrom. 2009 Mar;20(3):469-76. (PMID: 19056297)
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9528-33. (PMID: 15210983)
J Mass Spectrom. 2003 Feb;38(2):174-87. (PMID: 12577284)
Nucleic Acids Res. 2025 Jan 6;53(D1):D609-D617. (PMID: 39552041)
J Am Soc Mass Spectrom. 2010 Oct;21(10):1814-20. (PMID: 20688526)
J Proteome Res. 2021 Sep 3;20(9):4603-4609. (PMID: 34264676)
Contributed Indexing: Keywords: Mass Spectral Library; asparagine; cysteine; glutamine; proteomics
Substance Nomenclature: 0 (Ions)
0 (Peptide Library)
0 (Peptides)
Entry Date(s): Date Created: 20260714 Date Completed: 20260807 Latest Revision: 20260813
Update Code: 20260814
PubMed Central ID: PMC13459556
DOI: 10.1021/acs.jproteome.6c00094
PMID: 42447324
Βάση Δεδομένων: MEDLINE
FullText Text:
  Availability: 0
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DbLabel: MEDLINE
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PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
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  Data: Analysis and Annotation of c-Type Ions in Peptide Mass Spectral Libraries.
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  Data: <searchLink fieldCode="AU" term="%22Burke+MC%22">Burke MC</searchLink>; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States.<br /><searchLink fieldCode="AU" term="%22Yang+X%22">Yang X</searchLink>; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States.<br /><searchLink fieldCode="AU" term="%22Liang+Y%22">Liang Y</searchLink>; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States.<br /><searchLink fieldCode="AU" term="%22Neta+P%22">Neta P</searchLink>; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States.<br /><searchLink fieldCode="AU" term="%22Stein+SE%22">Stein SE</searchLink>; Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States.
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  Data: <searchLink fieldCode="JN" term="%22101128775%22">Journal of proteome research</searchLink> [J Proteome Res] 2026 Aug 07; Vol. 25 (8), pp. 4315-4321.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22American+Chemical+Society%22">American Chemical Society </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101128775 <i>Publication Model: </i>Print <i>Cited Medium: </i>Internet <i>ISSN: </i>1535-3907 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2215353893%22">15353893 </searchLink><i>NLM ISO Abbreviation: </i>J Proteome Res <i>Subsets: </i>MEDLINE
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  Data: <i>Original Publication</i>: Washington, D.C. : American Chemical Society, c2002-
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  Group: Su
  Data: <searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+chemistry%22">chemistry</searchLink> <br /><searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+analysis%22">analysis</searchLink> <br /><searchLink fieldCode="MM" term="%22Proteomics%22">Proteomics*</searchLink>/<searchLink fieldCode="MM" term="%22Proteomics+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Peptide+Library%22">Peptide Library*</searchLink><br /><searchLink fieldCode="MH" term="%22Ions%22">Ions</searchLink>/<searchLink fieldCode="MH" term="%22Ions+chemistry%22">chemistry</searchLink> ; <searchLink fieldCode="MH" term="%22Tandem+Mass+Spectrometry%22">Tandem Mass Spectrometry</searchLink>/<searchLink fieldCode="MH" term="%22Tandem+Mass+Spectrometry+methods%22">methods</searchLink> ; <searchLink fieldCode="MH" term="%22Humans%22">Humans</searchLink> ; <searchLink fieldCode="MH" term="%22Amino+Acid+Sequence%22">Amino Acid Sequence</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: The large collection of high-quality mass spectra in the NIST Human HCD Peptide and NIST Tandem Mass Spectral Libraries is used to understand the role of peptide sequence in c-type ion formation in beam-type collision-induced dissociation. Furthermore, results from the analyses were used to inform and apply annotation rules for c-type ions in the updated Human HCD Peptide Mass Spectral Library. As a result, 155,663 c-type ions are now annotated, providing additional peptide sequence information, often where b- and y-type ions may be lacking. Examples shown here highlight the significance of these c-type ions, both in terms of their relative abundance and in resolving peptide-sequence ambiguities. Furthermore, these examples illustrate the value of including c-type ions to improve searching and scoring of peptide spectrum matches.<br /> (Not subject to U.S. Copyright. Published 2026 by American Chemical Society.)
– Name: Ref
  Label: References
  Group: RefInfo
  Data: J Am Soc Mass Spectrom. 1993 Nov;4(11):874-31. (PMID: <searchLink fieldCode="PM" term="%2224227531%22">24227531)</searchLink><br />J Proteome Res. 2012 Nov 2;11(11):5479-91. (PMID: <searchLink fieldCode="PM" term="%2222998608%22">22998608)</searchLink><br />J Am Soc Mass Spectrom. 2013 Aug;24(8):1228-41. (PMID: <searchLink fieldCode="PM" term="%2223722727%22">23722727)</searchLink><br />Rapid Commun Mass Spectrom. 2004;18(18):2069-76. (PMID: <searchLink fieldCode="PM" term="%2215378720%22">15378720)</searchLink><br />Mass Spectrom Rev. 2009 Jul-Aug;28(4):640-54. (PMID: <searchLink fieldCode="PM" term="%2219338048%22">19338048)</searchLink><br />J Am Soc Mass Spectrom. 2009 Mar;20(3):469-76. (PMID: <searchLink fieldCode="PM" term="%2219056297%22">19056297)</searchLink><br />Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9528-33. (PMID: <searchLink fieldCode="PM" term="%2215210983%22">15210983)</searchLink><br />J Mass Spectrom. 2003 Feb;38(2):174-87. (PMID: <searchLink fieldCode="PM" term="%2212577284%22">12577284)</searchLink><br />Nucleic Acids Res. 2025 Jan 6;53(D1):D609-D617. (PMID: <searchLink fieldCode="PM" term="%2239552041%22">39552041)</searchLink><br />J Am Soc Mass Spectrom. 2010 Oct;21(10):1814-20. (PMID: <searchLink fieldCode="PM" term="%2220688526%22">20688526)</searchLink><br />J Proteome Res. 2021 Sep 3;20(9):4603-4609. (PMID: <searchLink fieldCode="PM" term="%2234264676%22">34264676)</searchLink>
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  Data: <i>Keywords: </i>Mass Spectral Library; asparagine; cysteine; glutamine; proteomics
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  Data: 0 (Ions)<br />0 (Peptide Library)<br />0 (Peptides)
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  Data: <i>Date Created: </i>20260714 <i>Date Completed: </i>20260807 <i>Latest Revision: </i>20260813
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  Data: 10.1021/acs.jproteome.6c00094
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  Data: 42447324
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=cmedm&AN=42447324
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        Value: 10.1021/acs.jproteome.6c00094
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        Text: English
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        StartPage: 4315
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      – SubjectFull: Tandem Mass Spectrometry methods
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      – SubjectFull: Peptide Library
        Type: general
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              Text: 2026 Aug 07
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