High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry.
A novel method for high-throughput proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMA) is described using on-tissue tryptic digestion followed by MALDI imaging MS. A TMA section containing 112 needle core biopsies from lung-tumor patients was analyzed using MS and the data were correlated to a serial hematoxylin and eosin (H&E)-stained section having various histological regions marked, including cancer, non-cancer, and normal ones. By correlating each mass spectrum to a defined histological region, statistical classification models were generated that can sufficiently distinguish biopsies from adenocarcinoma from squamous cell carcinoma biopsies. These classification models were built using a training set of biopsies in the TMA and were then validated on the remaining biopsies. Peptide markers of interest were identified directly from the TMA section using MALDI MS/MS sequence analysis. The ability to detect and characterize tumor marker proteins for a large cohort of FFPE samples in a high-throughput approach will be of significant benefit not only to investigators studying tumor biology, but also to clinicians for diagnostic and prognostic purposes.
Groseclose
M Reid
MR
Mass Spectrometry Research Center and Department of Chemistry and Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-8575, USA.
Massion
Pierre P
PP
Chaurand
Pierre
P
Caprioli
Richard M
RM
D000595:Amino Acid Sequence; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D008175:Lung Neoplasms / Q000737:chemistry* / Q000473:pathology; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000032:analysis*; D016612:Paraffin Embedding / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods; D046888:Tissue Array Analysis; D016707:Tissue Fixation / Q000379:methods
D005404:Fixatives; D009363:Neoplasm Proteins; D005557:Formaldehyde