title: Comparison of multiple protein extraction buffers for GeLC-MS/MS proteomic analysis of liver and colon formalin-fixed, paraffin-embedded tissues.
abstract: Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a potential valuable source of samples for clinical research. Since these specimens are banked in hospital archives, large cohorts of samples can be collected in short periods of time which can all be linked with a patients' clinical history. Therefore, the use of FFPE tissue in protein biomarker discovery studies gains interest. However, despite the growing number of FFPE proteome studies in the literature, there is a lack of a FFPE proteomics standard operating procedure (SOP). One of the challenging steps in the development of such a SOP is the ability to obtain an efficient and repeatable extraction of full length FFPE proteins. In this study, the protein extraction efficiency of eight protein extraction buffers is critically compared with GeLC-MS/MS (1D gel electrophoresis followed by in-gel digestion and LC-MS/MS). The data variation caused by using these extraction buffers was investigated since the variation is a very important aspect when using FFPE tissue as a source for biomarker detection. In addition, a qualitative comparison was made between the protein extraction efficiency and repeatability for FFPE tissue and fresh frozen tissue.
authors.affiliation: Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium. Valerie.Broeckx@bio.kuleuven.be.
authors.forename: Valérie
authors.initials: V
authors.lastname: Broeckx
authors.affiliation: Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium. Valerie.Broeckx@bio.kuleuven.be.
authors.forename: Kurt
authors.initials: K
authors.lastname: Boonen
authors.affiliation: Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium. Valerie.Broeckx@bio.kuleuven.be.
authors.forename: Lentel
authors.initials: L
authors.lastname: Pringels
authors.affiliation: Centre for Translational Cell and Tissue Research, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Xavier
authors.initials: X
authors.lastname: Sagaert
authors.affiliation: Department of Gastro-Enterology, Digestive Oncology Unit, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Hans
authors.initials: H
authors.lastname: Prenen
authors.affiliation: Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium. Valerie.Broeckx@bio.kuleuven.be.
authors.forename: Bart
authors.initials: B
authors.lastname: Landuyt
authors.affiliation: Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium. Valerie.Broeckx@bio.kuleuven.be.
authors.forename: Liliane
authors.initials: L
authors.lastname: Schoofs
authors.affiliation: Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium and Centre for Proteomics, University of Antwerp/Flemish Institute for Technological Research (VITO), Groenenborgerlaan 171, 2020 Antwerp, Belgium.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Maes
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002021:Buffers; D056148:Chromatography, Reverse-Phase; D003106:Colon / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D005557:Formaldehyde / Q000737:chemistry; D008099:Liver / Q000737:chemistry*; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D016612:Paraffin Embedding; D011499:Protein Processing, Post-Translational; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism; D040901:Proteomics; D053719:Tandem Mass Spectrometry; D016707:Tissue Fixation; D014357:Trypsin / Q000737:chemistry
chemical_list: D002021:Buffers; D020543:Proteome; D005557:Formaldehyde; D014357:Trypsin