MS-based proteomic classification of amyloidosis. Amyloid deposits were identified on Congo-red-stained paraffin sections under fluorescent light and microdissected with a laser. The microdissected amyloid fragments were then digested into tryptic peptides, separated by nano-flow liquid chromatography, ionized by electrospray ionization, and analyzed by tandem MS/MS. MS raw data files were queried by the use of three different algorithms (Mascot, Sequest, and X!Tandem), and the results were assigned peptide and protein probability scores. The proteins are listed according to the abundance with which they were represented in the sample based on spectral counting. The amyloid-forming protein identified is immunoglobulin lambda light chain (red boxes; Ig lambda chain constant and V-I regions), which is consistent with AL (lambda-type) amyloidosis. In addition, the samples contain several proteins known to be associated with amyloid deposits, such as apolipoprotein E and the serum amyloid P component, as well as stromal proteins such as actin, vitronectin, and vimentin. The identity and amounts of chaperone and fellow-traveler proteins cannot be precisely determined by any other technique and, once data are available on a large number of annotated cases, correlative analyses will likely reveal patterns of disease and progression linked to aspects of these accompanying proteins, such as proportions and polymorphisms. (Images courtesy of Dr. Ahmet Dogan, Mayo Clinic, Rochester, MN; dogan.ahmet@mayo.edu. See Vrana et al., 20094 for more information.)
