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Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

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The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include ⍺-cleavage and McLafferty rearrangement. Fragmentation by ⍺-cleavage preferentially occurs at the carbon-carbon bond at the ⍺-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their γ-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
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Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments
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UniCarb-DB: An MS/MS Experimental Glycomic Fragmentation Database.

Chunsheng Jin1, Vignesh Venkatakrishnan2, Kristina A Thomsson1

  • 1Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

Methods in Molecular Biology (Clifton, N.J.)
|July 12, 2024
PubMed
Summary
This summary is machine-generated.

UniCarb-DB is a glycomic spectral library that aids researchers in identifying glycan structures from mass spectrometry data. This resource facilitates glycomics research by providing a searchable database of tandem mass spectrometry (MS/MS) spectra.

Keywords:
DatabaseGlycan structureGlycomeOligosaccharidePosttranslational modificationSpectral libraryMass spectrometry

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Area of Science:

  • Glycomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Glycosylation is a critical posttranslational modification influencing cellular functions.
  • The glycome, encompassing all glycans in a cell or tissue, is complex and challenging to analyze.
  • Existing glycomic resources require efficient data management and analysis tools.

Purpose of the Study:

  • To introduce UniCarb-DB, a comprehensive spectral library for glycomics.
  • To provide mass spectrometry (MS) experimentalists with a tool for glycan structure elucidation.
  • To enhance the integration of glycomic data into research workflows.

Main Methods:

  • Development of a spectral library (UniCarb-DB) containing over 1500 entries of MS/MS fragment data.
  • Inclusion of metadata, experimental conditions, and biological origin for each entry.
  • Association of glycan structures with the GlyTouCan repository for broader resource access.

Main Results:

  • UniCarb-DB currently houses over 1000 unique glycan structures.
  • The database supports direct utilization by MS experimentalists for converting MS data into structural information.
  • Online search tools enable browsing isomeric structures and performing peak matching searches.

Conclusions:

  • UniCarb-DB significantly advances glycomics research by offering a robust spectral library.
  • The database facilitates quantitative and qualitative glycomics analysis through advanced MS tools.
  • UniCarb-DB is designed for seamless integration with commercial and open-access MS software.