PXD049965-1

PXD049965 is an original dataset announced via ProteomeXchange.

Title	Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques.
Description	The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identifications. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. Recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. SP4 has previously enriched low-solubility proteins, though differences in protein capture could affect which proteins are identified. We hypothesize that mechanisms of capture for SP3 and SP4 are distinct. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. Ultimately, we recommend clean-up techniques based on protein-sample hydrophobicity to yield high proteome coverage in biological samples.
HostingRepository	MassIVE
AnnounceDate	2024-05-27
AnnouncementXML	Submission_2024-05-27_17:02:23.731.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jessica Conforti
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine; S-carboxamidomethyl-L-cysteine
Instrument	Synapt G2-S HDMS; nanoACQUITY UPLC

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-20 08:11:45	ID requested
⏵ 1	2024-05-27 17:02:24	announced

no publication

submitter keyword: Proteomics, Sample Preparation, Mass Spectrometry, Single-Pot, Solid-Phase-Enhanced Sample Preparation (SP3), Solvent-Precipitation, Single-Pot, Solid-Phase-Enhanced Sample Preparation (SP4), Sodium Deoxycholate, Detergent-Assisted Digestion

Elyssia Gallagher
contact affiliation	Baylor University
contact email	elyssia_gallagher@baylor.edu
lab head
Jessica Conforti
contact affiliation	Baylor University
contact email	jess_conforti1@baylor.edu
dataset submitter

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/v07/MSV000094130/