PXD049062-2

PXD049062 is an original dataset announced via ProteomeXchange.

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

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.

10.1021/ACS.ANALCHEM.3C04479;

submitter keyword: proteomics, DIA,FFPE, rat, sample preparation, phosphoproteomics

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

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

• PRIDE
  1. PXD049062
     1. Label: PRIDE project
     2. Name: Quantitative comparison of deparaffinisation, rehydration and extraction methods for FFPE tissue proteomics and phosphoproteomics