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PXD064934-1
PXD064934 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Profiling Methylation in MCF7 Cells with Commercially Available SCX tips and Heavy-Methyl SILAC |
| Description | Methylation is an important post-translational modification that impacts cellular processes. Yet, methylation is difficult to detect with proteomics because it is less common compared to other modifications and often localized on low-abundance peptides. Although methylation does not alter physiochemical properties of amino acids, there is a reduced probability of trypsin cleavage after methylated lysine or arginine, leading to increased positive charges on methylated peptides. Strong-cation exchange (SCX) can be used to enrich methylated peptides. However, the number of methylation sites identified with SCX varies across previous studies, likely due to the use of different stationary phases and supports, elution strategies, and combinations of multiple enrichment techniques. Therefore, we hypothesize that commercially available SCX tips with a MS-friendly, ammonium-acetate elution can be used to enrich methylated peptides. Our results show that SCX effectively fractionates peptides by charge, which is associated with number of missed cleavages, and methylated peptides elute in fractions with high concentrations of ammonium acetate. When comparing SCX and no-enrichment methods, complementary methylation sites are identified, differing by sequence motifs. Ultimately, these results suggest that both SCX and no-enrichment methods may be required to effectively profile the methylome of complex biological samples. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-05-21 |
| AnnouncementXML | Submission_2026-05-21_11:07:21.202.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 | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; Methyl:2H(3)13C(1); Label:13C(1)2H(3); Dimethyl:2H(6)13C(2); unknown modification; unknown modification |
| Instrument | Orbitrap Fusion; instrument model |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-06-12 06:27:47 | ID requested | |
| ⏵ 1 | 2026-05-21 11:07:21 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Arginine methylation, Enrichment, Heavy-Methyl SILAC, Lysine methylation, Proteomics, Strong Cation Exchange, DatasetType:Proteomics |
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-ftp.ucsd.edu/v10/MSV000098142/ |
