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PXD032786-1

PXD032786 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSequence Coverage Visualizer: A web application for protein sequence coverage 3D visualization
DescriptionProtein structure is connected with its function and interaction and plays an extremely important role in protein characterization. As one of the most important analytical methods for protein characterization, Proteomics is widely used to determine protein composition, quantitation, interaction, and even structures. However, due to the gap between identified proteins by proteomics and available 3D structures, it was very challenging, if not impossible, to visualize proteomics results in 3D and further explore the structural aspects of proteomics experiments. Recently, two groups of researchers from DeepMind and Baker lab have independently published protein structure prediction tools that can help us obtain predicted protein structures for the whole human proteome. Although there is still debate on the validity of some of the predicted structures, it is no doubt that these represent the most accurate predictions to date. More importantly, this enabled us to visualize the majority of human proteins for the first time. To help other researchers best utilize these protein structure predictions, we present the Sequence Coverage Visualizer (SCV), http://scv.lab.gy, a web application for protein sequence coverage 3D visualization. Here we showed a few possible usages of the SCV, including the labeling of post-translational modifications and isotope labeling experiments. These results highlight the usefulness of such 3D visualization for proteomics experiments and how SCV can turn a regular result list into structural insights. Furthermore, when used together with limited proteolysis, we demonstrated that SCV can help validate and compare different protein structures, including predicted ones and existing PDB entries. By performing limited proteolysis on native proteins at various time points, SCV can visualize the progress of the digestion. This time-series data further allowed us to compare the predicted structure and existing PDB entries. Although not deterministic, these comparisons could be used to refine current predictions further and represent an important step towards a complete and correct protein structure database. Overall, SCV is a convenient and powerful tool for visualizing proteomics results.
HostingRepositoryPRIDE
AnnounceDate2022-12-14
AnnouncementXMLSubmission_2022-12-14_13:51:41.576.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterXinhaoShao
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-03-24 13:27:41ID requested
12022-12-14 13:51:41announced
22023-11-14 08:55:55announced2023-11-14: Updated project metadata.
Publication List
Keyword List
submitter keyword: proteomics, protein sequence coverage,3D structure, visualization
Contact List
Yu (Tom)Gao
contact affiliationDepartment of Pharmaceutical Sciences, University of Illinois at Chicago
contact emailyugao@uic.edu
lab head
XinhaoShao
contact affiliationUniversity of Illinois at Chicago
contact emailxshao8@uic.edu
dataset submitter
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Dataset FTP location
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