PXD020694

PXD020694 is an original dataset announced via ProteomeXchange.

Title	Data Independent Acquisition of plasma biomarkers of response to Neoadjuvant Chemotherapy in Pancreatic Ductal Adenocarcinoma
Description	The detection of disease-related plasma biomarkers has challenged the proteomic community for years. On the one hand there are many attractive features including the ease of collection and small volume needed for analysis, but on the other hand, the presence of high abundance proteins complicates technical sample preparation procedures and reduces proteome dynamic range. Data independent acquisition label free quantitation (DIA-LFQ) by mass spectrometry is an approach that partly overcomes the dynamic range issue; however, generating the peptide spectral reference libraries that allow extensive analysis of the plasma proteome can be a slow and expensive task which is unattainable for many laboratories. We investigated the re-purposing of publically available plasma proteome datasets and the impact on peptide/protein detection for DIA-LFQ. We carried out these studies in the context of pancreatic ductal adenocarcinoma, seeking biomarkers of response to neoadjuvant chemotherapy. We demonstrated the benefit in searching DIA data against multiple spectral libraries to show that complement activation was linked to response in these patients, confirming previous observations derived from proteomic analyses of PDAC tumours. Our workflow demonstrates that DIA-LFQ can be readily applied in the oncology setting for the putative assignment of clinically relevant plasma biomarkers.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:34:57.246.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew O'Rourke
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-03 02:39:35	ID requested
1	2022-03-02 03:10:35	announced
⏵ 2	2024-10-22 05:34:58	announced	2024-10-22: Updated project metadata.

O'Rourke MB, Sahni S, Samra J, Mittal A, Molloy MP, Data independent acquisition of plasma biomarkers of response to neoadjuvant chemotherapy in pancreatic ductal adenocarcinoma. J Proteomics, 231():103998(2021) [pubmed]

10.1016/j.jprot.2020.103998;

submitter keyword: complement, plasma, neoadjuvant chemotherapy, pancreatic cancer, biomarker,data-independent acquisition

Mark Molloy
contact affiliation	Kolling institute
contact email	m.molloy@sydney.edu.au
lab head
Matthew O'Rourke
contact affiliation	University of Technology Sydney
contact email	matthew.orourke1@gmail.com
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/2022/03/PXD020694

PRIDE project URI

• PRIDE
  1. PXD020694
     1. Label: PRIDE project
     2. Name: Data Independent Acquisition of plasma biomarkers of response to Neoadjuvant Chemotherapy in Pancreatic Ductal Adenocarcinoma