Evidence map›Paper›PMID 38995537›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

UniCarb-DB: An MS/MS Experimental Glycomic Fragmentation Database.

Chunsheng Jin, Vignesh Venkatakrishnan, Kristina A Thomsson, Nobuyuki P Aoki, Daisuke Shinmachi, Kiyoko F Aoki-Kinoshita, Catherine A Hayes, Frédérique Lisacek, Niclas G Karlsson

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Exploring the O-glycomic Degradome Using Natural Mucin Libraries.Methods in molecular biology (Clifton, N.J.) · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Chunsheng JinProteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Vignesh VenkatakrishnanDepartment of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
Kristina A ThomssonProteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Nobuyuki P AokiSoka University, Hachioji, Tokyo, Japan.
Daisuke ShinmachiSoka University, Hachioji, Tokyo, Japan.
Kiyoko F Aoki-KinoshitaSoka University, Hachioji, Tokyo, Japan.
Catherine A HayesProteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
Frédérique LisacekProteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
Niclas G KarlssonProteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. niclaska@oslomet.no.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Glycosylation is a unique posttranslational modification that dynamically shapes the surface of cells. Glycans attached to proteins or lipids in a cell or tissue are studied as a whole and collectively designated as a glycome. UniCarb-DB is a glycomic spectral library of tandem mass spectrometry (MS/MS) fragment data. The current version of the database consists of over 1500 entries and over 1000 unique structures. Each entry contains parent ion information with associated MS/MS spectra, metadata about the original publication, experimental conditions, and biological origin. Each structure is also associated with the GlyTouCan glycan structure repository allowing easy access to other glycomic resources. The database can be directly utilized by mass spectrometry (MS) experimentalists through the conversion of data generated by MS into structural information. Flexible online search tools along with a downloadable version of the database are easily incorporated in either commercial or open-access MS software. This chapter highlights UniCarb-DB online search tool to browse differences of isomeric structures between spectra, a peak matching search between user-generated MS/MS spectra and spectra stored in UniCarb-DB and more advanced MS tools for combined quantitative and qualitative glycomics.

Indexed as

GlycomicsPolysaccharidesSoftwareTandem Mass SpectrometryDatabases, FactualGlycosylationHumansPolysaccharidesDatabaseGlycan structureGlycomeMass spectrometryOligosaccharidePosttranslational modificationSpectral library

Identifiers

PMID38995537

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.