title: Efficient method for the proteomic analysis of fixed and embedded tissues.
abstract: Formalin-fixed and paraffin-embedded (FFPE) tissues present a particular challenge for proteomic analysis. Yet, most of the archived tissues in hospitals and tissue banks worldwide are only available in this form. We have developed conditions for removal of the embedding medium and protein digestion, such that informative tryptic peptides are released from fixed proteins which are suitable for analysis by liquid chromatography-mass spectrometry (LC-MS). We demonstrate that the peptide identifications made by this approach compare favorably to those made from matched fresh frozen tissue. Moreover, we demonstrate that a high level of sequence coverage can be observed for proteins of interest.
authors.affiliation: Harvard Partners Center for Genetics & Genomics, Cambridge, Massachusetts, USA.
authors.forename: Darryl Erik
authors.initials: DE
authors.lastname: Palmer-Toy
authors.forename: Bryan
authors.initials: B
authors.lastname: Krastins
authors.forename: David A
authors.initials: DA
authors.lastname: Sarracino
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Nadol
authors.forename: Saumil N
authors.initials: SN
authors.lastname: Merchant
mesh_terms: D000595:Amino Acid Sequence; D002853:Chromatography, Liquid; D015925:Cryopreservation; D005260:Female; D005404:Fixatives; D005557:Formaldehyde / Q000494:pharmacology; D006801:Humans; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010031:Otitis / Q000473:pathology; D010232:Paraffin / Q000494:pharmacology; D016612:Paraffin Embedding; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*; D013048:Specimen Handling; D013997:Time Factors; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D005404:Fixatives; D010455:Peptides; D005557:Formaldehyde; D010232:Paraffin