PXD022511

PXD022511 is an original dataset announced via ProteomeXchange.

Title	Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries
Description	Current methods for measuring amino-acid side-chain reactivity lack the throughput needed to screen large chemical libraries for interactions across the proteome. Here we redesigned the workflow for activity-based protein profiling of reactive cysteine residues by using a smaller desthiobiotin-based probe, sample multiplexing, reduced protein starting amounts, and software to boost data acquisition in real-time on the mass spectrometer. Our method, Streamlined Cysteine Activity-Based Protein Profiling (SLC-ABPP), achieved a 42-fold improvement in sample throughput, corresponding to profiling library members at a depth of >8,000 reactive cysteine sites in 18 min per compound. We applied it to identifying the proteome-wide targets of a covalent inhibitor of mutant KRASG12C and of ibrutinib, a covalent inhibitor of BTK. In addition, we created a resource of cysteine reactivity to 285 electrophiles in three human cell lines , which includes >20,000 cysteines in >6,000 proteins per cell line. The goal of proteome-wide profiling of cysteine reactivity across thousand-member libraries under several cellular contexts is now within reach.
HostingRepository	PRIDE
AnnounceDate	2021-01-26
AnnouncementXML	Submission_2021-01-25_22:59:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miljan Kuljanin
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetic acid derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-13 03:13:42	ID requested
⏵ 1	2021-01-25 22:59:07	announced

Kuljanin M, Mitchell DC, Schweppe DK, Gikandi AS, Nusinow DP, Bulloch NJ, Vinogradova EV, Wilson DL, Kool ET, Mancias JD, Cravatt BF, Gygi SP, Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries. Nat Biotechnol, 39(5):630-641(2021) [pubmed]

submitter keyword: chemical proteomics, reactive cysteines

Steven P. Gygi
contact affiliation	Department of Cell Biology, Harvard Medical School, Boston MA, USA
contact email	steven_gygi@hms.harvard.edu
lab head
Miljan Kuljanin
contact affiliation	Harvard Medical School
contact email	miljan_kuljanin@hms.harvard.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/2021/01/PXD022511

PRIDE project URI

• PRIDE
  1. PXD022511
     1. Label: PRIDE project
     2. Name: Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries