PXD020808

PXD020808 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometric detection of proteins associated with lymph node metastasis in T1/2 colorectal cancer from FFPE archival specimens
Description	Surgical resection of colorectal cancers (CRC) that have not invaded beyond the bowel wall (i.e. Stage I) can achieve 5-year patient survival rates exceeding 90%. In the majority of Stage I cases with T1 (submucosal) or T2 (not beyond the muscularis propria) depth of tumour invasion, surgery alone is curative. However, for approximately 10% of resected T1/2 CRC, even though histopathology inspection of the tumour deems it to be restricted to the bowel wall, malignant cells are identified in draining lymph nodes, signifying local metastasis. These patients are classified with Stage IIIA disease and are at greater risk than Stage I patients whose tumours show similar invasive depth, but lack lymph node involvement. To counter the risk of distant malignant dissemination, Stage IIIA patients require more extensive treatment with adjuvant chemotherapy, while Stage I patients do not. In this study we aim to get a better understanding of the underlying biological pathways linked to lymph node metastasis (LNM) using discovery based MS (DIA) and RNASeq as well as IHC and PRM to verify possible protein marker. All of this was done on archival tissue samples (FFPE).
HostingRepository	PRIDE
AnnounceDate	2021-01-14
AnnouncementXML	Submission_2021-01-14_00:47:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pascal Steffen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-08 17:00:50	ID requested
⏵ 1	2021-01-14 00:47:48	announced

Steffen P, Li J, Chandra J, Ahadi MS, Gill AJ, Engel AF, Molloy MP, Molecular Features of Lymph Node Metastasis in T1/2 Colorectal Cancer from Formalin-Fixed Paraffin-Embedded Archival Specimens. J Proteome Res, 20(2):1304-1312(2021) [pubmed]

submitter keyword: DIA, FFPE, colorectal cancer, PRM

Mark P. Molloy
contact affiliation	The University of Sydney, Department of Medicine & Health, Kolling Institute
contact email	m.molloy@sydney.edu.au
lab head
Pascal Steffen
contact affiliation	The University of Sydney
contact email	pascal.steffen@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/2021/01/PXD020808

PRIDE project URI

• PRIDE
  1. PXD020808
     1. Label: PRIDE project
     2. Name: Mass spectrometric detection of proteins associated with lymph node metastasis in T1/2 colorectal cancer from FFPE archival specimens