Comprehensive identification of proteins from MALDI imaging

Stefan K. Maier, Hannes Hahne, Amin Moghaddas Gholami, Benjamin Balluff, Stephan Meding, Cedrik Schoene, Axel K. Walch, Bernhard Kuster

Research output: Contribution to journalArticlepeer-review

69 Scopus citations


Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a generic method that removes this issue by systematically identifying the proteins embedded in the MALDI matrix using a combination of bottom-up and top-down proteomics. The analyses of ten human tissues lead to the identification of 1400 abundant and soluble proteins constituting the set of proteins detectable by MALDI IMS including >90% of all IMS biomarkers reported in the literature. Top-down analysis of the matrix proteome identified 124 mostly N- and C-terminally fragmented proteins indicating considerable protein processing activity in tissues. All protein identification data from this study as well as the IMS literature has been deposited into MaTisse, a new publically available database, which we anticipate will become a valuable resource for the IMS community.

Original languageEnglish
Pages (from-to)2901-2910
Number of pages10
JournalMolecular and Cellular Proteomics
Issue number10
StatePublished - Oct 2013


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