title: Integrated and Quantitative Proteomics of Human Tumors.
abstract: Quantitative proteomics represents a powerful approach for the comprehensive analysis of proteins expressed under defined conditions. These properties have been used to investigate the proteome of disease states, including cancer. It has become a major subject of studies to apply proteomics for biomarker and therapeutic target identification. In the last decades, technical advances in mass spectrometry have increased the capacity of protein identification and quantification. Moreover, the analysis of posttranslational modification (PTM), especially phosphorylation, has allowed large-scale identification of biological mechanisms. Even so, increasing evidence indicates that global protein quantification is often insufficient for the explanation of biology and has shown to pose challenges in identifying new and robust biomarkers. As a consequence, to improve the accuracy of the discoveries made using proteomics in human tumors, it is necessary to combine (i) robust and reproducible methods for sample preparation allowing statistical comparison, (ii) PTM analyses in addition to global proteomics for additional levels of knowledge, and (iii) use of bioinformatics for decrypting protein list. Herein, we present technical specificities for samples preparation involving isobaric tag labeling, TiO2-based phosphopeptides enrichment and hydrazyde-based glycopeptides purification as well as the key points for the quantitative analysis and interpretation of the protein lists. The method is based on our experience with tumors analysis derived from hepatocellular carcinoma, chondrosarcoma, human embryonic intervertebral disk, and chordoma experiments.
authors.affiliation: MUMC+ Maastricht, The Netherlands; MHeNs, Experimental Neurosurgery, Maastricht University, Maastricht, The Netherlands.
authors.forename: Y
authors.initials: Y
authors.lastname: Yakkioui
authors.affiliation: MUMC+ Maastricht, The Netherlands; MHeNs, Experimental Neurosurgery, Maastricht University, Maastricht, The Netherlands.
authors.forename: Y
authors.initials: Y
authors.lastname: Temel
authors.affiliation: Inserm ERL440 Oncogenesis, Stress, Signaling, Université de Rennes 1, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
authors.forename: E
authors.initials: E
authors.lastname: Chevet
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Strasbourg University, Illkirch, France. Electronic address: luc.negroni@igbmc.fr.
authors.forename: L
authors.initials: L
authors.lastname: Negroni
mesh_terms: D000818:Animals; D002851:Chromatography, High Pressure Liquid; D006020:Glycopeptides / Q000737:chemistry / Q000302:isolation & purification; D006801:Humans; D009363:Neoplasm Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D009369:Neoplasms / Q000737:chemistry* / Q000378:metabolism; D010748:Phosphopeptides / Q000737:chemistry / Q000302:isolation & purification; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics; D020539:Sequence Analysis, Protein; D053719:Tandem Mass Spectrometry
chemical_list: D006020:Glycopeptides; D009363:Neoplasm Proteins; D010748:Phosphopeptides; D020543:Proteome
keywords: Chordoma; Hepatocellular carcinoma; Mass spectrometry; Solid tumors; iTRAQ