PXD033780

PXD033780 is an original dataset announced via ProteomeXchange.

Title	Evaluation of a Pooling Chemoproteomics Strategy with an FDA-approved Drug Library
Description	Chemoproteomics is a key platform for characterizing the mode of action (MoA) for compounds, especially for targeted protein degraders such as proteolysis targeting chimerics (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle up to 18 samples in a single experiment. Here, we present a pooling strategy to further enhance the throughput, and apply the strategy to an FDA-approved drug library (95 best-in-class compounds). The TMT-MS-based pooling strategy was evaluated in the following steps. First, we demonstrated the capability of TMT-MS by analyzing over 15,000 unique proteins (>12,000 gene products) in HEK293 cells treated with five PROTACs (two BRD/BET degraders and three degraders for FAK, ALK, and BTK kinases). We then introduced a rationalized pooling strategy to separate structurally similar compounds in different pools, and identified the proteomic response to 14 pools from the drug library. Finally, we validated the proteomic response from one pool by re-profiling the cells under individual drug treatment with sufficient replicates. Interestingly, numerous proteins were found to change upon drug treatment, including AMD1, ODC1, PRKX, PRKY, EXO1, AEN and LRRC58 by 7-Hydroxystaurosporine; C6orf64, HMGCR and RRM2 by Sorafenib; SYS1 and ALAS1 by Venetoclax; and ATF3, CLK1 and CLK4 by Palbocilib. Thus, the pooling chemoproteomics screening provides an efficient method for dissecting the molecular targets of compound libraries.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:43:06.733.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	huan sun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-09 05:37:25	ID requested
1	2023-03-11 06:48:13	announced
⏵ 2	2023-11-14 08:43:15	announced	2023-11-14: Updated project metadata.

Sun H, Yang K, Zhang X, Fu Y, Yarbro J, Wu Z, Chen PC, Chen T, Peng J, Evaluation of a Pooling Chemoproteomics Strategy with an FDA-Approved Drug Library. Biochemistry, 62(3):624-632(2023) [pubmed]

submitter keyword: mass spectrometry

proteomics

chemoproteomics

tandem mass tag

pooling strategy

PROTAC

molecular glue

targeted protein degeneration

FDA library

Junmin Peng
contact affiliation	St.jude children's research hospital
contact email	junmin.peng@stjude.org
lab head
huan sun
contact affiliation	St.Jude Children's Research Hospital
contact email	huansun0@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033780
     1. Label: PRIDE project
     2. Name: Evaluation of a Pooling Chemoproteomics Strategy with an FDA-approved Drug Library