PXD011971 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Comparison of proteomic and phospho-proteomic analysis upon urea extraction and triple extraction |
Description | The goal of the present project was to investigate the applicability of a triple extraction (”TE”), which yields RNA, DNA and protein in a single procedure, for gel-free mass spectrometry-based proteomics. Proven successful for large-scale transcriptomics and genomics, we examined TE compatibility with mass spectrometry-based proteomics and phospho-proteomics by comparison to a urea standard processing. For whole proteome, peptides were fractionated using SAX; for phosphorylation analysis, modifications were enriched using TiO2 columns. We here demonstrate the efficiency of TE protocol for shotgun proteomics, providing similar results as urea-derived samples both at the qualitative and quantitative levels. The study of phosphorylation events is likewise compatible with TE, which actually results in a higher number of correctly localized sites than urea, while the nature of extracted sites appears somewhat distinct between both techniques. We thus conclude that our protocol is well suited for proteomics and as efficient as other more widely used workflows for mass spectrometry-based analysis. |
HostingRepository | PRIDE |
AnnounceDate | 2021-07-20 |
AnnouncementXML | Submission_2021-07-19_21:58:00.448.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Guillaume Arras |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Fusion |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-12-07 01:07:39 | ID requested | |
⏵ 1 | 2021-07-19 21:58:01 | announced | |
Publication List
Sanchez-Quiles V, Shi MJ, Dingli F, Krucker C, Loew D, Bernard-Pierrot I, Radvanyi F, Triple extraction method enables high quality mass spectrometry-based proteomics and phospho-proteomics for eventual multi-omics integration studies. Proteomics, 21(16):e2000303(2021) [pubmed] |
Keyword List
curator keyword: Technical, Biomedical |
submitter keyword: SAX, TiO2, urea, triple extraction, bladder cancer |
Contact List
Damarys Loew |
contact affiliation | Laboratoire de Spectrometrie de Masse Proteomique Institut Curie PSL Research University |
contact email | Damarys.Loew@curie.fr |
lab head | |
Guillaume Arras |
contact affiliation | Institut Curie |
contact email | guillaume.arras@curie.fr |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD011971
- Label: PRIDE project
- Name: Comparison of proteomic and phospho-proteomic analysis upon urea extraction and triple extraction