PXD032786

PXD032786 is an original dataset announced via ProteomeXchange.

Title	Sequence Coverage Visualizer: A web application for protein sequence coverage 3D visualization
Description	Protein 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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:55:55.340.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xinhao Shao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-24 13:27:41	ID requested
1	2022-12-14 13:51:41	announced
⏵ 2	2023-11-14 08:55:55	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: proteomics, protein sequence coverage,3D structure, visualization

Yu (Tom) Gao
contact affiliation	Department of Pharmaceutical Sciences, University of Illinois at Chicago
contact email	yugao@uic.edu
lab head
Xinhao Shao
contact affiliation	University of Illinois at Chicago
contact email	xshao8@uic.edu
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2022/12/PXD032786

PRIDE project URI

• PRIDE
  1. PXD032786
     1. Label: PRIDE project
     2. Name: Sequence Coverage Visualizer: A web application for protein sequence coverage 3D visualization