title: An experimental guideline for the analysis of histologically heterogeneous tumors by MALDI-TOF mass spectrometry imaging.
abstract: Mass spectrometry imaging (MSI) has been widely used for the direct molecular assessment of tissue samples and has demonstrated great potential to complement current histopathological methods in cancer research. It is now well established that tissue preparation is key to a successful MSI experiment; for histologically heterogeneous tumor tissues, other parts of the workflow are equally important to the experiment's success. To demonstrate these facets here we describe a matrix-assisted laser desorption/ionization MSI biomarker discovery investigation of high-grade, complex karyotype sarcomas, which often have histological overlap and moderate response to chemo-/radio-therapy. Multiple aspects of the workflow had to be optimized, ranging from the tissue preparation and data acquisition protocols, to the post-MSI histological staining method, data quality control, histology-defined data selection, data processing and statistical analysis. Only as a result of developing every step of the biomarker discovery workflow was it possible to identify a panel of protein signatures that could distinguish between different subtypes of sarcomas or could predict patient survival outcome. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Sha
authors.initials: S
authors.lastname: Lou
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Maastricht MultiModal Molecular Imaging institute (M4I), Maastricht University, Maastricht, The Netherlands.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Balluff
authors.affiliation: Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Arjen H G
authors.initials: AHG
authors.lastname: Cleven
authors.affiliation: Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Judith V M G
authors.initials: JVMG
authors.lastname: Bovée
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands; Fondazione Pisana per la Scienza ONLUS, Pisa, Italy. Electronic address: L.A.Mcdonnell@lumc.nl.
authors.forename: Liam A
authors.initials: LA
authors.lastname: McDonnell
mesh_terms: D015415:Biomarkers / Q000378:metabolism; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis* / Q000378:metabolism / Q000473:pathology*; D012509:Sarcoma / Q000175:diagnosis / Q000378:metabolism / Q000473:pathology; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods
chemical_list: D015415:Biomarkers
keywords: Biomarker discovery; High grade sarcoma; Mass spectrometry imaging; Protocol optimization