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PXD038077

PXD038077 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDyakov_etal_Nuclear_Bodies_BioID_Map_2023
DescriptionThis dataset consists of the files for 334 BioID samples: .wiff and .wiff.scan raw MS files, .mzML peak files, and MSPLIT results files; all acquired on TripleTOF 6600 mass spectrometers operated in Data Independent Acquisition mode (SWATH). It also includes the sequence database used for analysis and the MSPLIT spectral library which was generated from paired samples acquired in Data Dependent Acquisition (DDA) mode. All sample generation, streptavidin affinity purification, mass spectrometric acquisition, and data analysis was performed by Boris Dyakov. 13 of the stable cell lines used in this study were generated in Anne-Claude Gingras’ lab by Ji-Young Youn and Wade Dunham (Lunenfeld-Tanenbaum Research Institute); 6 of the stable cell lines were generated in Eric Shoubridge’s lab (McGill University) by Hana Antonicka. The files are associated with a manuscript submitted for publication by Dyakov et al. that provides a spatial map of nuclear body-associated proteins with a focus on the paraspeckle and nuclear speckle. Refer to the corresponding table in the published manuscript for a full description of all baits used; 36/146 baits included in this dataset were previously used in earlier publications and collaborations from our group. Anne-Claude Gingras is the corresponding author of the manuscript and should be contacted for questions about this dataset (gingras@lunenfeld.ca).
HostingRepositoryMassIVE
AnnounceDate2024-07-02
AnnouncementXMLSubmission_2024-07-02_23:07:04.254.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterGingras Lab
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListL-methionine sulfoxide
InstrumentTripleTOF 6600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-09 15:36:05ID requested
12024-07-02 23:07:04announced
Publication List
no publication
Keyword List
submitter keyword: BioID, Proximity-dependent biotinylation, protein-protein interaction, spatial map, HEK293, Nuclear bodies, Condensates, Nucleus, Paraspeckle, Nuclear speckle, Nucleolus, Cajal body, PML body
Contact List
Anne-Claude Gingras
contact affiliationLTRI
contact emailgingras@lunenfeld.ca
lab head
Gingras Lab
contact affiliationSamuel Lunenfeld Research Institute
contact emailgingras@mshri.on.ca
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/v05/MSV000090684/