PXD000383

PXD000383 is an original dataset announced via ProteomeXchange.

Title	QUEST-MS for plasma biomarkers complementing the specificity of PSA test
Description	To explore plasma biomarkers complementing the specificity of PSA test, we developed a unique proteomic technology QUEST-MS (Quick Enrichment of Small Targets for Mass Spectrometry). The QUEST-MS method based on 96-well formatted sequential reversed phase chromatography allowing efficient enrichment of < 20 kDa proteins quickly and reproducibly. The LC/MS/MS data from 24 healthy controls, 19 benign prostate hypertrophy (BPH) patients, and 73 prostate cancer patients plasma were subjected to label-free quantification analysis on Expressionist proteome server. Data processing: Mascot Server 2.3.1 was used with the database SwissProt 2011_08 (531473 sequences,188463640 residues). Enzyme: semiTrypsin. Search parameters: Peptide Mass Tolerance : +- 3 ppm, Fragment Mass Tolerance:+-0.8 Da. Fixed modifications:Carbamidomethyl (C). Variable modifications:Oxidation (M),Deamidated (NQ). Max Missed Cleavages:2.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-08-08_05:44:16.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000383
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Koji Ueda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	instrument model: LTQ-Orbitrap-Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-30 03:50:24	ID requested
1	2014-01-28 03:26:53	announced
2	2014-07-28 00:43:15	announced	Updated project metadata.
⏵ 3	2014-08-08 05:44:17	announced	Updated project metadata.

Ueda K, Tatsuguchi A, Saichi N, Toyama A, Tamura K, Furihata M, Takata R, Akamatsu S, Igarashi M, Nakayama M, Sato TA, Ogawa O, Fujioka T, Shuin T, Nakamura Y, Nakagawa H, Plasma low-molecular-weight proteome profiling identified neuropeptide-Y as a prostate cancer biomarker polypeptide. J Proteome Res, 12(10):4497-506(2013) [pubmed]

submitter keyword: Human, Plasma

Koji Ueda
contact affiliation	Laboratory for Biomarker Development
contact email	k-ueda@riken.jp
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/2014/01/PXD000383

PRIDE project URI

• PRIDE
  1. PXD000383
     1. Label: PRIDE project
     2. Name: QUEST-MS for plasma biomarkers complementing the specificity of PSA test