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PXD017324 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePINE: An Automation Tool to Extract & Visualize Functionally Enriched Networks from Mass Spectrometry-Based Proteomics Datasets
DescriptionRecent surges in mass spectrometry-based proteomics studies demands a concurrent rise in speedy and optimized data processing tools and pipelines. While several stand-alone databases exist that store gene interaction and annotation information, we developed Protein Interaction Network Extractor (PINE) as a fully-automated, user-friendly, graphical interface-based bioinformatics tool that has an easily adoptable framework suitable for study of all proteins and post-translational modifications (PTMs) sites enabling simple, quick and robust visualization of differentially expressed proteins or PTMs and their interaction or functionally enriched networks. PINE tool can be applied not only to better understand protein functional interaction networks but also to analyze PTMs involved and their effect. To illustrate the relevance of the tool, we explore the total proteome and its PTM -associated relationships in two different nonalcoholic steatohepatitis (NASH) mouse models to show different context-specific use cases. The strength of this tool relies in its ability to (1) perform accurate protein identifier mapping to resolve any ambiguity, (2) retrieve interaction data from multiple publicly available protein-protein interaction databases, (3) assimilate these complex networks into meaningful functionally enriched pathways. Ultimately this tool can be used as an extremely powerful approach for novel hypothesis generation towards understanding disease mechanisms and potential therapeutics.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterVidya Venkatraman
SpeciesList scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationListPhospho; Carbamidomethyl; Oxidation
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-01-29 14:17:40ID requested
12021-02-23 10:12:40announced
Publication List
Sundararaman N, Go J, Robinson AE, Mato JM, Lu SC, Van Eyk JE, Venkatraman V, PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks. J Am Soc Mass Spectrom, 31(7):1410-1421(2020) [pubmed]
Keyword List
submitter keyword: Proteomics, data visualization, enriched networks, automated bioinformatics tool, post-translational modifications
Contact List
Jennifer Van Eyk
contact affiliationCedars-Sinai Medical Center
contact emailjennifer.vaneyk@cshs.org
lab head
Vidya Venkatraman
contact affiliationCedars-Sinai Medical Center
contact emailvidya.venkatraman@cshs.org
dataset submitter
Full Dataset Link List
Panorama Public dataset URI