PXD001725

PXD001725 is an original dataset announced via ProteomeXchange.

Title	A Protein Deep Sequencing Evaluation of Metastatic Melanoma Tissues, unfractionated approach
Description	Malignant melanoma has currently the highest increase of incidence of malignancies in the western world. In early stages, front line therapy is surgical excision of the primary tumor. Metastatic disease has previously has very limited possibilities to be cured. Recently, several protein kinase inhibitors and immune modifiers have shown promising results but drug resistance in metastasized melanoma remains a major problem. The need for clinical biomarkers to follow disease progression and treatment effects is high. The aim of the present study was to build a protein sequence database in metastatic melanoma, searching for novel, relevant biomarkers. Ten lymph node metastases (South-Swedish Malignant Melanoma Biobank) were subjected to global protein expression analysis using two proteomics approaches (with/without orthogonal fractionation). Fractionation produced higher numbers of protein identifications (4284). Combining both methods, 5326 unique proteins were identified (2641 proteins overlapping). Deep mining proteomics may contribute to the discovery of novel biomarkers for metastatic melanoma, for example dividing the samples into two metastatic melanoma "genomic subtypes", ("pigmentation" and "high immune") revealed several proteins showing differential levels of expression. In conclusion, the present study provides an initial version of a metastatic melanoma protein sequence database producing a total of more than 5000 unique protein identifications. This dataset consists of data for ten samples. A sister dataset, consisting of four samples (that are included in the current ten), was analysed , analysed by applying strong cation exchange chromatography (SCX) step before the MS step.
HostingRepository	PRIDE
AnnounceDate	2015-04-17
AnnouncementXML	Submission_2015-04-17_04:29:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Krzysztof Pawlowski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-23 06:35:33	ID requested
⏵ 1	2015-04-17 04:29:44	announced

Welinder C, Paw, ł, owski K, Sugihara Y, Yakovleva M, J, ö, nsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Jansson B, Laurell T, Fehniger T, D, ö, me B, Malm J, Wieslander E, Nishimura T, Marko-Varga G, A protein deep sequencing evaluation of metastatic melanoma tissues. PLoS One, 10(4):e0123661(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: Malignant Melanoma, lymph node metastases

György Marko-Varga
contact affiliation	Clinical Protein Science & Imaging, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
contact email	gyorgy.marko-varga@bme.lth.se
lab head
Krzysztof Pawlowski
contact affiliation	Lund University and Warsaw University of Life Sciences
contact email	krzysztof_pawlowski@sggw.pl
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/2015/04/PXD001725

PRIDE project URI

• PRIDE
  1. PXD001725
     1. Label: PRIDE project
     2. Name: A Protein Deep Sequencing Evaluation of Metastatic Melanoma Tissues, unfractionated approach