PXD008698

PXD008698 is an original dataset announced via ProteomeXchange.

Title	Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics
Description	The broad variability in protein and peptide biochemistry necessitates robust protocols and reagents for efficiently handling these molecules prior to analysis with mass spectrometry (MS) or other techniques. In this study, further exploration of the paramagnetic bead-based approach, Single-Pot Solid-Phase-Enhanced Sample Preparation (SP3), is carried out. The SP3 approach was tested in a wide range of experimental scenarios, including: 1. Binding solvents (acetonitrile, ethanol, isopropanol, acetone); 2. Binding pH (acidic vs. neutral/basic); 3. Solvent/lysate ratios (50% - 200%, v/v); 4. Mixing and rinsing conditions (on-rack vs. off-rack rinsing); 5. Enrichment of non-denatured proteins; 6. Enrichment of individual proteins from non-complex mixtures. These results highlight the robust handling of proteins in a broad set of scenarios, while also enabling development of a modified SP3 workflow that offers extended functionality. The modified SP3 approach is used in quantitative in-depth proteome analyses to compare it with commercial paramagnetic bead-based HILIC methods (MagReSyn) and across multiple binding conditions (e.g. pH and solvent during binding). Together, these data reveal the extensive quantitative coverage of the proteome possible with SP3 independent of the binding approach utilized. The results further establish the utility of SP3 for the unbiased handling of peptides and proteins for proteomic applications.
HostingRepository	PRIDE
AnnounceDate	2018-03-28
AnnouncementXML	Submission_2018-03-28_00:34:58.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008698
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Hughes
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Ammonia-loss; Glu->pyro-Glu; TMT6plex; Oxidation; Acetyl; Carbamidomethyl; Gln->pyro-Glu
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-17 01:00:20	ID requested
⏵ 1	2018-03-28 00:34:59	announced

Moggridge S, Sorensen PH, Morin GB, Hughes CS, Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics. J Proteome Res, 17(4):1730-1740(2018) [pubmed]

curator keyword: Technical

submitter keyword: SP3, HILIC, mass spectrometry, protein clean-up, TMT

Gregg Morin
contact affiliation	Head of Proteomics
contact email	gmorin@bcgsc.ca
lab head
Christopher Hughes
contact affiliation	British Columbia Cancer Research Centre
contact email	chughes@bcgsc.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008698
     1. Label: PRIDE project
     2. Name: Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics