High-coverage quantitative proteomics using amine-specific isotopic labeling.
Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.
Melanson
Jeremy E
JE
Institute for Marine Biosciences, National Research Council of Canada, Halifax, Nova Scotia, Canada.
Avery
Steven L
SL
Pinto
Devanand M
DM
D000544:Alzheimer Disease / Q000378:metabolism*; D000588:Amines / Q000737:chemistry*; D000595:Amino Acid Sequence; D000818:Animals; D001921:Brain / Q000378:metabolism; D002417:Cattle; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D007553:Isotope Labeling; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D040901:Proteomics; D012710:Serum Albumin, Bovine / Q000032:analysis; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization
D000588:Amines; D012710:Serum Albumin, Bovine