GPMDB00175OtherWelinder C, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humangyorgy.marko-varga@bme.lth.se25874936http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310019272http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310019253http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310019266http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310019246http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310019259Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden, et al.Not availableGPMDBMalignant melanoma has 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 very limited possibilities for cure. Recently, several protein kinase inhibitors and immune modifiers have shown promising clinical results but drug resistance in metastasized melanoma remains a major problem. The need for routine clinical biomarkers to follow disease progression and treatment efficacy 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. The raw data have been deposited to the ProteomeXchange with identifiers PXD001724 and PXD001725.A protein deep sequencing evaluation of metastatic melanoma tissues.Welinder Charlotte C,Pawłowski Krzysztof K,Sugihara Yutaka Y,Yakovleva Maria M,Jönsson Göran G,Ingvar Christian C,Lundgren Lotta L,Baldetorp Bo B,Olsson Håkan H,Rezeli Melinda M,Jansson Bo B,Laurell Thomas T,Fehniger Thomas T,Döme Balazs B,Malm Johan J,Wieslander Elisabet E,Nishimura Toshihide T,Marko-Varga György G,Welinder Charlotte C, Pawłowski Krzysztof K, Sugihara Yutaka Y, Yakovleva Maria M, Jönsson Göran G, Ingvar Christian C, Lundgren Lotta L, Baldetorp Bo B, Olsson Håkan H, Rezeli Melinda M, Jansson Bo B, Laurell Thomas T, Fehniger Thomas T, Döme Balazs B, Malm Johan J, Wieslander Elisabet E, Nishimura Toshihide T, Marko-Varga György Gpolypeptide, deep, proteins, Tissue.APR, Viral Marker, Biological Markers, Surrogate Endpoints, HSN1E, determination, Clinical Markers, Laboratory, Clinical Marker, Biochemical, malignant melanoma NOS (morphologic abnormality), APOER, EA1, Endpoint, MLR-3, Serum, Malignant, Surrogate End Points, Surrogate Markers, Laboratory Markers, AIM, CD91, Biological, Malignant melanoma (morphologic abnormality), malignant melanoma (disorder), Melanosarcoma, early activation antigen CD69, study, Entire lymph node, Clinical, activation inducer molecule, NOXA, Biological Marker, Naevocarcinoma, present in organism, proteins, leukocyte surface antigen Leu-23, Immunologic Markers, Immune, Markers, A2MR, [M]Malignant melanoma NOS (morphologic abnormality), no ICD-O subtype (morphologic abnormality), Viral Markers, [M]Malignant melanoma NOS, LRP1A, C-type lectin domain family 2 member C, Immunologic Marker, Biologic, close to, data, Viral, Surrogate Endpoint, LRP, lymphatic system, Serum Markers, DNMT, End Point, Biochemical Markers, Malignant Melanomas, MCMT, Biologic Marker, Immune Marker, MM - Malignant melanoma, near to, BL-AC/P26, polypeptide, Melanomas, Experiment, Melanoma, Marker, Surrogate End Point, Malignant Melanoma, chemical analysis, sequence, TGFBR5, NOS, morphology (morphologic abnormality), Data Base, nodus lymphaticus, Biologic Markers, CXXC9, early T-cell activation antigen p60, ADCADN, Serum Marker, End Points, Surrogate, Endpoints, Immunologic, Malignant melanoma, Laboratory Marker, primary structure of sequence macromolecule, Surrogate Marker, Lymph node, no ICD-O subtype, GP32/28, Biochemical Marker, approaches, vicinity of., lymph gland, assay, CD69, CLEC2C, IGFBP3R, Immune Markerspolypeptide, deep, proteins, Tissue.Bru, advanced, Viral Marker, Biological Markers, protein kinase inhibitors, Surrogate Endpoints, Procedures, Raw, HSN1E, determination, chromatophore, Clinical Markers, Laboratory, Incidences, Clinical Marker, chromatocyte, Neoplasms, drug susceptibility/resistance, malignant melanoma NOS (morphologic abnormality), Biochemical, Endpoint, EA1, Gene, Tumor, Serum, MLR-3, Malignant, temporal, NEOPL, Surrogate End Points, Surrogate Markers, Laboratory Markers, AIM, Kinase Inhibitors, Biological, Method, Studies, Gene Products, Malignant melanoma (morphologic abnormality), Inhibitors, malignant melanoma (disorder), Del(8)44H, Melanosarcoma, early activation antigen CD69, drug resistance, Progression, treatment, Svc, study, human disease, Entire lymph node, Clinical, activation inducer molecule, Naevocarcinoma, Biological Marker, tumour, present in organism, proteins, procedures, Study, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), Immunologic Markers, leukocyte surface antigen Leu-23, Immune, Markers, Methodological Studies, [M]Malignant melanoma NOS (morphologic abnormality), no ICD-O subtype (morphologic abnormality), data., Viral Markers, [M]Malignant melanoma NOS, disease management, C-type lectin domain family 2 member C, Homo sapiens disease, Immunologic Marker, Neoplastic Growth, incidence, Biologic, Tumors, close to, Disease, Viral, Surrogate Endpoint, lymphatic system, Serum Markers, Proteins, Disease Exacerbation, DNMT, End Point, Biochemical Markers, Malignant Melanomas, MCMT, Procedure, Biologic Marker, tumours, results, Immune Marker, MM - Malignant melanoma, near to, Progressions, BL-AC/P26, polypeptide, Melanomas, Melanoma, Marker, Surrogate End Point, Pigmentations, Malignant Melanoma, Protein, chemical analysis, Diseases, precocious, Resistance, sequence, NOS, techniques, morphology (morphologic abnormality), Data Base, nodus lymphaticus, Biologic Markers, CXXC9, Disease Progressions, early T-cell activation antigen p60, deep, ADCADN, Serum Marker, Col4a-1, End Points, pigment cell, Surrogate, Endpoints, Malignant melanoma, Immunologic, Methodological, pigment cells, Laboratory Marker, Methodological Study, Surrogate Marker, primary structure of sequence macromolecule, early, Drug, Protein Gene Products, Gene Proteins, pigments, metastatic, Lymph node, no ICD-O subtype, GP32/28, Biochemical Marker, approaches, vicinity of, biological pigment, pigmentation, lymph gland, assay, Protein Kinase, CD69, NEOPLASMS BENIGN, Neoplasia, CLEC2C, methodology, Immune Markers1705http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310019253dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0052436767427513880.01.0falseA Protein Deep Sequencing Evaluation of Metastatic Melanoma Tissues.Data from ProteomeXchange, .PXD ID: PXD001724. Experiment: M35_003, file: folder summary. Published as part of PLoS One. 2015 Apr 13;10(4):e0123661 . From the Abstract: {{i}} ... 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).... {{/i}}2015-04-21GPM3231001925325874936PXD001724PXD001724