Analyst PAPER Cite this: Analyst, 2016, 141, 3403 Received 19th January 2016, Accepted 19th April 2016 DOI: 10.1039/c6an00126b www.rsc.org/analyst Aluminium foil as a single-use substrate for MALDI-MS fingerprinting of different melanoma cell lines† A. Bondarenko, a Y. Zhu, a L. Qiao, a F. Cortés Salazar, a H. Pick b and H. H. Girault* a Herein, we present the intact cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the fingerprinting of human melanoma cancer cell lines grown on aluminium foil. To perform the MALDI-MS assay, melanoma cells were cultured on a flat and thin foil, which was directly transferred to the target plate of MALDI-MS for analysis. The influence of a wide range of cell fixation pro- tocols (i.e. formalin-based and alcohol-based methods) and MALDI matrices on the obtained character- istic spectra was investigated. For the optimization of the MALDI-MS protocol, the MS fingerprints of the melanoma WM-239 cell line with and without an overexpressed enhanced green fluorescent protein were employed. The fingerprints obtained from WM-239 cells grown on aluminium foil were compared with the intact cell MALDI-MS of the cell pellet and presented higher sensitivity in a high m/z range. The optimized protocol was subsequently applied to characterise melanoma cell lines derived from different cancer stages and allowed identification of unique MS signals that could be used for differentiation between the studied cell lines (i.e. molecular weight equal to 10.0 kDa and 26.1 kDa). Introduction Mammalian cells cultured in vitro have been widely employed in medicine and biology as a simple model of complex living organisms to develop new strategies for diagnosis and treatment of different diseases. 1–4 With this aim various approaches to characterize cells have been developed based on chemical sensing, optical microscopy and mass-spectrometry (MS). 5–9 In comparison with other strategies, MS is a label free technique where the analytical signal depends on the mole- cular weight and charge of the analysed species after ioniza- tion. Typically, MS experiments for the characterization of in vitro cultured cells include cell lysis followed by the MS ana- lysis of the obtained extract with or without enzymatic protein cleavage. 10 However, the full cell proteome analysis is very chal- lenging and therefore, MS is often combined with separation techniques, i.e. electrophoresis or liquid chromatography. 11 To ionize cellular constituents without fragmentation, soft ioniza- tion techniques, e.g. electrospray ionization (ESI) 12 and matrix- assisted laser desorption/ionization (MALDI) 13,14 are widely used. 15–18 Although these methods allow the detection and identification of a wide range of proteins with high sensitivity, they are complex and time-consuming. Another approach for analysis of in vitro cultured mamma- lian cells is the intact cell (IC) analysis, typically performed by MALDI-MS. In this case, cells can be either grown directly on a MALDI target plate 19 or collected by centrifugation after cultur- ing in a classical Petri dish. 11,20–23 The latter allows cell pellets to be either transferred directly to the target plate, where they are dried and covered with a matrix solution, 22,24 or mixed with a matrix solution prior to the transfer. 20,21,23,25,26 As a result, instead of individual protein peaks, a number of signals representing the MS fingerprint characteristic for a specific cell type or physiological state can be obtained. 11 This approach has been successfully applied for the identification of two different pancreatic cell lines, 22 the differentiation between stimulated and non-stimulated macrophages, 20 differ- entiation of toxic effects generated by different compounds, 24 the prediction of mammalian cell phenotypes, 21 the rapid detection of apoptosis in mammalian cells, 26 the monitoring of histone deacetylase drug target engagement 25 and the characterization of neural cell types. 23 Moreover, it was reported that the analysis of on-target-grown cells resulted in mass spectra of higher peak intensity in comparison with the protocols with whole cells placed on top of a matrix layer and with cellular extracts analysed using the conventional † Electronic supplementary information (ESI) available. See DOI: 10.1039/ c6an00126b a Laboratoire d’Electrochimie Physique et Analytique, École Polytechnique Fédérale de Lausanne, EPFL Valais Wallis, CH-1951 Sion, Switzerland. E-mail: hubert.girault@epfl.ch b Laboratoire de Chimie Physique des Polymères et Membranes, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland This journal is © The Royal Society of Chemistry 2016 Analyst, 2016, 141, 3403–3410 | 3403