Protocol to analyze 1D and 2D mass spectrometry data from glioblastoma tissues for cancer diagnosis and immune cell identification.

STAR Protoc

University Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France. Electronic address:

Published: September 2024

In context of cancer diagnosis-based mass spectrometry (MS), the classification model created is crucial. Moreover, exploration of immune cell infiltration in tissues can offer insights within the tumor microenvironment. Here, we present a protocol to analyze 1D and 2D MS data from glioblastoma tissues for cancer diagnosis and immune cells identification. We describe steps for training the most optimal model and cross-validating it, for discovering robust biomarkers and obtaining their corresponding boxplots as well as creating an immunoscore based on MS-imaging data. For complete details on the use and execution of this protocol, please refer to Zirem et al..

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11408140PMC
http://dx.doi.org/10.1016/j.xpro.2024.103285DOI Listing

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