title: A protein deep sequencing evaluation of metastatic melanoma tissues.
abstract: Malignant 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.
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden; Centre of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden.
authors: Charlotte
authors: C
authors: Welinder
authors: Warsaw University of Life Sciences, Warsaw, Poland.
authors: Krzysztof
authors: K
authors: Pawłowski
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden.
authors: Yutaka
authors: Y
authors: Sugihara
authors: National Korányi Institute of Pulmonology, Budapest, Hungary; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden.
authors: Maria
authors: M
authors: Yakovleva
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden.
authors: Göran
authors: G
authors: Jönsson
authors: Surgery, Dept. of Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden.
authors: Christian
authors: C
authors: Ingvar
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden.
authors: Lotta
authors: L
authors: Lundgren
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden.
authors: Bo
authors: B
authors: Baldetorp
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden; Skåne University Hospital, Lund, Sweden; Cancer Epidemiology, Dept. of Clinical Sciences, Lund University, Lund, Sweden.
authors: Håkan
authors: H
authors: Olsson
authors: Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden.
authors: Melinda
authors: M
authors: Rezeli
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden.
authors: Bo
authors: B
authors: Jansson
authors: Centre of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden.
authors: Thomas
authors: T
authors: Laurell
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden; Centre of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden.
authors: Thomas
authors: T
authors: Fehniger
authors: National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.
authors: Balazs
authors: B
authors: Döme
authors: Section for Clinical Chemistry, Dept. of Laboratory Medicine, Lund University, Skåne University Hospital in Malmö, Malmö, Sweden.
authors: Johan
authors: J
authors: Malm
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden.
authors: Elisabet
authors: E
authors: Wieslander
authors: Oncology and Pathology, Dept. of Clinical Sciences, Lund University, Lund, Sweden; Centre of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden; First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan.
authors: Toshihide
authors: T
authors: Nishimura
authors: Centre of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, Lund, Sweden; First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan.
authors: György
authors: G
authors: Marko-Varga
mesh_terms: D018070:Biological Specimen Banks; D002853:Chromatography, Liquid; D019295:Computational Biology; D057225:Data Mining; D030562:Databases, Protein; D019008:Drug Resistance, Neoplasm; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008207:Lymphatic Metastasis; D008545:Melanoma / Q000378:metabolism*; D009362:Neoplasm Metastasis; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D012878:Skin Neoplasms / Q000378:metabolism*; D013548:Sweden; D053719:Tandem Mass Spectrometry; D000096142:Cutaneous Malignant Melanoma