PXD065035

PXD065035 is an original dataset announced via ProteomeXchange.

Title	KM-12 Whole Cell Lysate Proteomics
Description	The KM-12 cell line, representative of colorectal cancer indications, was used to explore the effect that multiple compounds would have in the profile of transcription factor occupancy. Cells were dosed with 3 concentrations of each of the 5 compounds provided for 3 different timepoints. Both a chromatin fraction (ChESS) and a whole cell lysate preparation were performed. Resulting proteins were digested via SP3 digestion and resulting peptides were analyzed by data independent acquisition liquid chromatography mass spectrometry. (DIA-LCMS) in order to determine the effects of each of the provided compounds in both chromatin and whole cell lysate matrices on a variety of transcription factor proteins. The following dataset includes data corresponding to peptides resulting from nuclear isolation after a 6 hour treatment with 100 nanomolar concentration CG-428 (positive control, published TRK PROTAC), JWJ-378 (novel PROTAC developed by Nabet lab), and DMSO (negative control).
HostingRepository	PRIDE
AnnounceDate	2026-04-06
AnnouncementXML	Submission_2026-04-05_18:36:24.287.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sebastian Paez
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Ultra 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-15 20:34:43	ID requested
⏵ 1	2026-04-05 18:36:25	announced

10.1039/d6cb00008h;

Kumar S, Jiang J, Donald-Paladino MS, Chen J, Gutierrez A, Federation AJ, Szulzewsky F, Holland EC, Ferguson FM, Nabet B, Development of PROTACs for targeted degradation of oncogenic TRK fusions. RSC Chem Biol, 7(4):596-614(2026) [pubmed]

submitter keyword: LC-MSMS,Colorectal Cancer, timsTOF

Alexander Federation
contact affiliation	Talus Bio
contact email	afederation@talus.bio
lab head
Sebastian Paez
contact affiliation	Talus Bioscience
contact email	spaez@talus.bio
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/2026/04/PXD065035

PRIDE project URI

• PRIDE
  1. PXD065035
     1. Label: PRIDE project
     2. Name: KM-12 Whole Cell Lysate Proteomics