PXD067680-1
PXD067680 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability |
| Description | Cell function studies primarily focus on measuring overall molecular abundances while often overlooking critical clues—including protein modifications and molecular interaction networks—that critically determine the functional properties of the cell. In prior work, we introduced a suite of methods to reveal context-specific transcription factor-gene regulatory networks, kinase-substrate networks, and protein interaction networks and leveraged them to gain deeper insights into transcriptional regulation and signal transduction. However, the complex interdependencies between these networks are still elusive. To address this challenge, we introduce a multi-omics framework, aimed at harnessing measured or inferred protein activity in context-specific networks, which yields deeper functional insights into mechanisms underlying molecular phenotypes, compared to protein abundance alone. As proof of concept, we utilized progressively differentiated instances of HeLa CCL2 and Kyoto cell lines to explore the role of protein complexes and interactions in cell doubling time and susceptibility to Salmonella Typhimurium infection. Notably, this analysis underscores the pivotal role of protein interaction networks in linking molecular profiles to phenotypic outcomes, thus providing a highly generalizable framework for multi-omics dataset analysis. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-09-25 |
| AnnouncementXML | Submission_2025-09-25_12:49:51.925.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | George Rosenberger |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Acetyl; Oxidation; Carbamidomethyl |
| Instrument | TripleTOF 5600+ |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-08-24 23:41:20 | ID requested | |
| ⏵ 1 | 2025-09-25 12:49:52 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: DIA, SWATH, SEC, Size-Exclusion Chromatography, Data-independent Acquisition, SEC-SWATH-MS, DatasetType:Proteomics |
Contact List
| Ruedi Aebersold | |
|---|---|
| contact affiliation | Institute of Molecular Systems Biology, ETH Zurich |
| contact email | aebersold@imsb.biol.ethz.ch |
| lab head | |
| George Rosenberger | |
| contact affiliation | Columbia University |
| contact email | george@rosenberger.pro |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v10/MSV000098930/ |
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