PXD049062 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Quantitative comparison of deparaffinisation, rehydration and extraction methods for FFPE tissue proteomics and phosphoproteomics |
Description | Formalin-fixed paraffin-embedded tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The sample preparation method chosen influences the number, intensity, and reproducibility of identifications. By comparing the performance of four deparaffinisation and rehydration methods, we found that heptane and methanol quantified the most protein groups whilst the most widely used xylene and ethanol quantified the least. We then modified five extraction methods from the literature based on their diverse lysis and digestion conditions before evaluating their performance using rat organs of the kidney, leg muscle, lung, and testis. All methods performed well except for SP3, that struggled with tissue lysis. Heat n’ Beat was the fastest, had the highest digestion efficiency, quantified protein groups, and lowest coefficient of variation across replicates. Strap produced the highest peptide yield and SPEED produced a ultraviolet quantitation interference. TFE produced the highest phosphoprecursor intensity with a 10-15% higher enrichment efficiency. We demonstrate that the choice of extraction method has a larger impact on the phosphoproteome than the proteome. We conclude by providing recommendations for choosing the most appropriate method for different settings. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:52:40.332.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Erin Humphries |
SpeciesList | scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; |
ModificationList | phosphorylated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-01-31 20:14:11 | ID requested | |
1 | 2024-08-06 04:58:32 | announced | |
⏵ 2 | 2024-10-22 06:52:40 | announced | 2024-10-22: Updated project metadata. |
Publication List
Keyword List
submitter keyword: proteomics, DIA,FFPE, rat, sample preparation, phosphoproteomics |
Contact List
Phillip J. Robinson |
contact affiliation | ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia. |
contact email | probinson@cmri.org.au |
lab head | |
Erin Humphries |
contact affiliation | The University of Sydney |
contact email | ehum9128@uni.sydney.edu.au |
dataset submitter | |
Full Dataset Link List
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://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD049062 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD049062
- Label: PRIDE project
- Name: Quantitative comparison of deparaffinisation, rehydration and extraction methods for FFPE tissue proteomics and phosphoproteomics