⮝ Full datasets listing

PXD060303

PXD060303 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMapping the nanoscale organization of the human cell surface proteome reveals uncharacterized functional associations and surface antigen clusters
DescriptionThe cell surface is a dynamic interface central to immune activation, cell-cell communication, and signal transduction. Despite its functional significance, the spatial organization of cell surface proteins remains poorly understood. High-resolution fluorescence microscopy and proximity labeling have advanced studies of surface protein arrangement, but a systematic analysis of the spatial organization of the complete surface proteome remains unexplored. In this study, we systematically mapped the surface proteome of human T-lymphocytes and B-lymphoblasts using proximity labeling of 85 antigens, identified from over 100 antibodies tested for binding to surface-exposed proteins. These experiments were coupled with an optimized data-independent acquisition (DIA) mass spectrometry workflow to generate a robust dataset. Unsupervised clustering of the resulting interactome revealed functional modules, including well-characterized complexes such as the T-cell receptor and HLA class I/II, alongside novel clusters. Notably, we identified mitochondrial proteins localized to the surface, including the transcription factor TFAM, suggesting previously unappreciated roles for mitochondrial proteins at the plasma membrane. A high-accuracy machine learning classifier predicted over 6,000 surface protein associations, highlighting functional associations such as IL10RBs role as a negative regulator of type I interferon signaling. Spatial modeling of the surface proteome provided insights into protein dispersion patterns, distinguishing widely distributed proteins, such as CD45, from localized antigens, such as CD226. Interestingly, protein distribution appeared independent of abundance, pointing to active mechanisms regulating surface organization. This work provides a comprehensive map of the human surfaceome, offering a resource for exploring the spatial and functional dynamics of the cell membrane proteome.
HostingRepositoryMassIVE
AnnounceDate2025-02-12
AnnouncementXMLSubmission_2025-02-12_16:44:31.252.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterBrendan Floyd
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListOxidation; Carbamidomethyl; Acetyl
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02025-01-28 20:33:37ID requested
12025-02-12 16:44:31announced
Publication List
no publication
Keyword List
submitter keyword: Surfaceomics, Membrane, Proximity labeling, DatasetType:Proteomics
Contact List
Carolyn Bertozzi
contact affiliationStanford University
contact emailbertozzi@stanford.edu
lab head
Brendan Floyd
contact affiliationStanford University
contact emailbmfloyd@stanford.edu
lab head
Brendan Floyd
contact affiliationStanford University
contact emailbmfloyd@stanford.edu
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.ucsd.edu/v09/MSV000096983/