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However, if the morphological organization of the organ can be addressed, then, in the best case, the composition of molecules in single cells of the target organ can be analyzed. Laser capture microdissection (LCM) is a technique which enables the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming two-dimensional technique, and optimal results are only obtained if the tissue is fixed, e.g., by formalin. Especially for proteome analysis, formalin fixation reduced the number of identifiable proteins, and this is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study, the applicability of the infrared laser tissue sampling for the proteome analysis of different cell layers of murine intestine was investigated, using LC\u2013MS\/MS-based differential quantitative bottom-up proteomics. By laser ablation, eight consecutive layers of colon tissue were obtained and analyzed. However, a clear distinguishability of protein profiles between ascending, descending, and transversal colon was made, and we identified the different intestinal-cell-layer proteins, which are cell-specific, as confirmed by data from the Human Protein Atlas. Thus, for the first time, sampling directly from intact fresh-frozen tissue with three-dimensional resolution is giving access to the different proteomes of different cell layers of colon tissue.<\/jats:p>","DOI":"10.3390\/ijms23116132","type":"journal-article","created":{"date-parts":[[2022,5,30]],"date-time":"2022-05-30T10:05:14Z","timestamp":1653905114000},"page":"6132","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine"],"prefix":"10.3390","volume":"23","author":[{"given":"Hannah","family":"Vo\u00df","sequence":"first","affiliation":[{"name":"Section\/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8537-7493","authenticated-orcid":false,"given":"Manuela","family":"Moritz","sequence":"additional","affiliation":[{"name":"Section\/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Penelope","family":"Pelczar","sequence":"additional","affiliation":[{"name":"Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola","family":"Gagliani","sequence":"additional","affiliation":[{"name":"Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"},{"name":"Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9325-8227","authenticated-orcid":false,"given":"Samuel","family":"Huber","sequence":"additional","affiliation":[{"name":"Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivien","family":"Nippert","sequence":"additional","affiliation":[{"name":"Section\/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9358-7036","authenticated-orcid":false,"given":"Hartmut","family":"Schl\u00fcter","sequence":"additional","affiliation":[{"name":"Section\/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3416-636X","authenticated-orcid":false,"given":"Jan","family":"Hahn","sequence":"additional","affiliation":[{"name":"Section\/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistra\u00dfe 52, 20246 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,5,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41580-020-0259-3","article-title":"Human organoids: Model systems for human biology and medicine","volume":"21","author":"Kim","year":"2020","journal-title":"Nat. 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