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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/15970

Title: Proteomic analysis of formalin-fixed paraffin-embedded colorectal cancer tissue using tandem mass tag protein labeling
Authors: Maes, Evelyne
Valkenborg, Dirk
Mertens, Inge
Broeckx, Valerie
Baggerman, Geert
Sagaert, Xavier
Landuyt, Bart
Prenen, Hans
Schoofs, Liliane
Issue Date: 2013
Citation: MOLECULAR BIOSYSTEMS, 9 (11), p. 2686-2695
Abstract: In clinical research, repositories of biological samples form a rich source of clinical material for biomarker studies. Banked material, however, is often not stored in optimal conditions regarding the technology used for biomarker research. A case in point is formalin-fixed paraffin-embedded (FFPE) tissue that could be used to obtain large cohorts of samples over a short period of time, as these tissues are routinely prepared for pathological analysis. However, in the context of mass spectrometry based peptide-centric proteomics, protein extraction and identification can be hampered by formalin-induced crosslinking. Furthermore, the molecular formalin crosslinks might be entangled differently across various samples, making it more difficult to reproducibly extract the same proteins from different samples. In this study, we establish the crosslink variability using Tandem Mass Tag (TMT) protein labeling followed by digestion, separation, identification and quantification of proteins extracted from FFPE colorectal cancer and paired healthy tissues. Moreover, by applying de novo interpretation of tandem mass spectra and subsequent analysis by Peaks PTM, unspecified modifications could be elucidated, leading to increased protein and proteome coverage. This approach might be useful for future FFPE proteomics studies.
URI: http://hdl.handle.net/1942/15970
DOI: 10.1039/c3mb70177h
ISI #: 000325401800011
ISSN: 1742-206X
Category: A1
Type: Journal Contribution
Validation: ecoom, 2014
Appears in Collections: Research publications

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