PXD040903
PXD040903 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Chapter 5: Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification, Compartment and Process Coverage, and Enables More Reflective Protein-Level Label-Free Quantitation |
| Description | The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Within, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition method. Analysis of offline fractionated cell line digests using both separations revealed increase peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. |
| HostingRepository | MassIVE |
| AnnounceDate | 2023-03-15 |
| AnnouncementXML | Submission_2023-03-15_19:00:38.306.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Graham Delafield |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Acetyl; Oxidation; Deamidated |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-03-15 17:10:53 | ID requested | |
| ⏵ 1 | 2023-03-15 19:00:38 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Porous Graphitic Carbon, Data Completeness, Sample Coverage |
Contact List
| Lingjun Li | |
|---|---|
| contact affiliation | University of Wisconsin-Madison |
| contact email | lingjun.li@wisc.edu |
| lab head | |
| Graham Delafield | |
| contact affiliation | University of Wisconsin - Madison |
| contact email | delafield@wisc.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/MSV000091495/ |
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