PXD000704

PXD000704 is an original dataset announced via ProteomeXchange.

Title	Glycoprotein Signatures for Aggressive Prostate Cancer via SWATH mass spectrometry
Description	The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) addresses an urgent clinical need to minimize the general over-treatment of patients with non-aggressive PCa, which account for the majority of PCa cases. In this study we combined N-glycopeptide isolation and SWATH-MS towards the molecular characterization of tumor malignancy and aggressiveness. Here, we isolated formerly N-linked glycopeptides from normal prostate (n=10), non-aggressive (n=22), aggressive (n=16) and metastatic PCa (n=25) tumor tissues and analyzed the samples by SWATH-MS, an emerging data independent mass spectrometric acquisition method that generates a single MS file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy where a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH-MS data. On-average we identified 1430 N-glycosites from each SWATH map of which 1057 were quantified across all samples. The 220 glycoproteins that showed significant quantitative changes associated diverse biological processes with the level of PCa aggressiveness and metastasis and indicated functional relationships with common PCa genomic mutations.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:49:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yansheng Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deaminated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2014-01-22 04:57:06	ID requested
1	2014-04-23 08:02:39	announced
2	2014-04-24 00:49:05	announced	Updated publication reference for PubMed record(s): 24741114.
⏵ 3	2014-07-24 03:49:29	announced	Updated project metadata.

Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R, Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics, 13(7):1753-68(2014) [pubmed]

curator keyword: Biomedical, Technical

submitter keyword: Human, Prostate, Glycoproteome, SWATH

Ruedi Aebersold
contact affiliation	Institute of Molecular Systems Biology, ETH Zurich
contact email	aebersold@imsb.biol.ethz.ch
lab head
Yansheng Liu
contact affiliation	Institute of Molecular Systems Biology, ETH Zurich
contact email	liu@imsb.biol.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000704
     1. Label: PRIDE project
     2. Name: Glycoprotein Signatures for Aggressive Prostate Cancer via SWATH mass spectrometry