PXD059224

PXD059224 is an original dataset announced via ProteomeXchange.

Title	Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding
Description	Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecules by DNA sequencing. However, the solution properties of individual protein molecules cannot be probed using such approaches because they are completely altered by DNA attachment. Mass spectrometry enables parallel evaluation of protein properties amenable to physical fractionation such as solubility and oligomeric state, but current approaches are limited to libraries of 1,000 or fewer proteins. Here, we improved mass spectrometry barcoding by co-synthesizing proteins with barcodes optimized to be highly multiplexable and minimally perturbative, scaling to libraries of >5,000 proteins. We use these barcodes together with mass spectrometry to assay the solution behavior of libraries of de novo-designed monomeric scaffolds, oligomers, binding proteins and nanocages, rapidly identifying design failure modes and successes.
HostingRepository	PanoramaPublic
AnnounceDate	2024-12-24
AnnouncementXML	Submission_2024-12-24_20:35:03.202.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jeremiah Sims
SpeciesList	scientific name: Escherichia coli BL21(DE3); NCBI TaxID: 469008;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-24 19:35:51	ID requested
⏵ 1	2024-12-24 20:35:03	announced

Dataset with its publication pending

submitter keyword: barcoding, peptide, size exclusion chromatography, SEC, protein design, RFDiffusion, generative design, deep learning, machine learning, DL, ML

David Baker
contact affiliation	University of Washington
contact email	dabaker@uw.edu
lab head
Jeremiah Sims
contact affiliation	University of Washington
contact email	simsjn@uw.edu
dataset submitter

Panorama Public dataset URI