Emilio Marengo 1 Elisa Robotti 1 Marco Bobba 1 Maria Cristina Liparota 1 Chiara Rustichelli 2 Alberto Zamò 3 Marco Chilosi 3 Pier Giorgio Righetti 2 1 Department of Environmental and Life Sciences, University of Eastern Piedmont, Alessandria, Italy 2 Scientific and Technological Department, University of Verona, Verona, Italy 3 Department of Pathology, University of Verona, Verona, Italy Received April 27, 2005 Revised September 20, 2005 Accepted September 20, 2005 Research Article Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis Mantle cell lymphoma (MCL) cell lines have been difficult to generate, since only few have been described so far and even fewer have been thoroughly characterized. Among them, there is only one cell line, called GRANTA-519, which is well established and universally adopted for most lymphoma studies. We succeeded in establishing a new MCL cell line, called MAVER-1, from a leukemic MCL, and performed a thorough phenotypical, cytogenetical and molecular characterization of the cell line. In the present report, the phenotypic expression of GRANTA-519 and MAVER-1 cell lines has been compared and evaluated by a proteomic approach, exploiting 2-D map analysis. By univariate statistical analysis (Student’s t-test, as commonly used in most com- mercial software packages), most of the protein spots were found to be identical be- tween the two cell lines. Thirty spots were found to be unique for the GRANTA-519, whereas another 11 polypeptides appeared to be expressed only by the MAVER-1 cell line. A number of these spots could be identified by MS. These data were confirmed and expanded by multivariate statistical tools (principal component analysis and soft- independent model of class analogy) that allowed identification of a larger number of differently expressed spots. Multivariate statistical tools have the advantage of reduc- ing the risk of false positives and of identifying spots that are significantly altered in terms of correlated expression rather than absolute expression values. It is thus sug- gested that, in future work in differential proteomic profiling, both univariate and multi- variate statistical tools should be adopted. Keywords: 2-D gel electrophoresis / Human lymphoma / Principal component analy- sis / Soft-independent model of class analogy DOI 10.1002/elps.200500323 1 Introduction 1.1 General aspects It is commonly acknowledged that 2-DE is one of the most exploited techniques for the separation of proteins in biological samples, i.e., biological fluids, cellular extracts and tissue samples [1]. Proteomic 2-D PAGE maps are acquiring crucial impor- tance as diagnostic/prognostic tools in the study of genetic pathologies and they can be exploited for unra- velling the mechanism of action of many diseases, since the incidence of particular pathologies is related to the presence/absence of some proteins or to the change of their relative quantitative ratio in cellular extracts. The application of the proteomic approach to the investi- gation of different diseases is widely reported in literature: brain diseases have been studied by Fountoulakis [2] in the last few years. Many studies have also appeared on the investigation of protein extracts of tumoural cells: among them, the most recent ones report the application of proteomic techniques to the study of lymphoma [3], Correspondence: Professor Emilio Marengo, Department of Envi- ronmental and Life Sciences, University of Eastern Piedmont, Via Bellini 25/G, I-15100 Alessandria, Italy E-mail: marengoe@tin.it Fax: 139-0131-360390 Abbreviations: MCL, mantle cell lymphoma; PCA, principal compo- nent analysis; PC, principal components; SIMCA, soft-indipendent model of class analogy; SSP , standard spot number; TCTP , transi- tionally controlled tumour protein 484 Electrophoresis 2006, 27, 484–494 * Present Address: Polytecnic of Milano, Dept. of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Milano, Italy  2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.electrophoresis-journal.com