PXD024684 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs (data set D1) |
Description | Motivation: 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 two underlying organisms (mouse and yeast) 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= |
HostingRepository | PRIDE |
AnnounceDate | 2021-07-30 |
AnnouncementXML | Submission_2021-07-30_02:02:40.947.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD024684 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Karin Schork |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | Ammonia-loss; 2-pyrrolidone-5-carboxylic acid (Gln); Ammonium; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-03-11 08:11:14 | ID requested | |
⏵ 1 | 2021-07-30 02:02:41 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Mus musculus, spike-in, label-free |
Contact List
Martin Eisenacher |
contact affiliation | Ruhr-University Bochum, Medical Faculty, Medizinisches Proteom-Center, Medical Bioinformatics Ruhr-University Bochum, Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) |
contact email | martin.eisenacher@rub.de |
lab head | |
Karin Schork |
contact affiliation | Medizinisches Proteom-Center, Ruhr-University Bochum |
contact email | karin.schork@rub.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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- PRIDE
- PXD024684
- Label: PRIDE project
- Name: Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs (data set D1)