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PXD049965

PXD049965 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDifferences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques.
DescriptionThe 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.
HostingRepositoryMassIVE
AnnounceDate2024-05-27
AnnouncementXMLSubmission_2024-05-27_17:02:23.731.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJessica Conforti
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListL-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine; S-carboxamidomethyl-L-cysteine
InstrumentSynapt G2-S HDMS; nanoACQUITY UPLC
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-02-20 08:11:45ID requested
12024-05-27 17:02:24announced
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 affiliationBaylor University
contact emailelyssia_gallagher@baylor.edu
lab head
Jessica Conforti
contact affiliationBaylor University
contact emailjess_conforti1@baylor.edu
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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