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PXD030603

PXD030603 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCharacterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs - data set D3 (without and with isoforms)
DescriptionMotivation: In bottom-up mass spectrometry proteins are enzymatically digested before measurement. The relationship between proteins and peptides can be represented by bipartite graphs that can be split into connected components. This representation is useful to aid protein inference and quantification, which is complex due to the occurrence of shared peptides. We conducted a comprehensive analysis of these bipartite graphs using peptides from an in silico digestion of protein databases as well as quantified peptides. Results: The graphs based on quantified peptides are smaller and have less complex structures compared to the database level. However, the proportion of protein nodes without unique peptides and the proportion of graphs that contain these proteins increase. Large differences between the different underlying organisms on database as well as quantitative level could be observed. Insights of this analysis may be useful for the development of protein inference and quantification algorithms. Link to preprint: https://www.biorxiv.org/content/10.1101/2021.07.28.454128v1?ct=
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_07:18:32.060.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKarin Schork
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-12-22 07:31:19ID requested
12022-11-11 02:01:33announced
22023-11-14 07:18:34announced2023-11-14: Updated project metadata.
Publication List
Schork K, Turewicz M, Uszkoreit J, Rahnenf, ΓΌ, hrer J, Eisenacher M, Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs. PLoS One, 17(10):e0276401(2022) [pubmed]
Keyword List
submitter keyword: Human, E.Coli
Contact List
Martin Eisenacher
contact affiliationRuhr-University Bochum, Medical Faculty, Medizinisches Proteom-Center, Medical Bioinformatics. Ruhr-University Bochum, Medical Proteome Analysis, Center for Proteindiagnostics (PRODI).
contact emailmartin.eisenacher@rub.de
lab head
Karin Schork
contact affiliationMedizinisches Proteom-Center, Ruhr-University Bochum
contact emailkarin.schork@rub.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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