PXD049965
PXD049965 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2024-02-20 08:11:45 | ID requested | |
⏵ 1 | 2024-05-27 17:02:24 | announced |
Publication List
no publication |
Keyword List
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 |
Contact List
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 |
Full Dataset Link List
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/ |