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The development of isobaric tagging chemistries has permitted measurements in relative protein expression across several samples with a high degree of automation. Recently, a new set of isobaric reagents was developed that expanded the number of channels that can be processed simultaneously from four to eight. This doubling of the unique isobaric tags increases flexibility in the design of a multiplexing experiment, allowing the incorporation of a greater number of experimental samples, duplicates, or additional controls into a single pooled sample.
Described herein is a method to use these reagents to measure relative protein expression across several cerebral spinal fluid (CSF) samples. Eight control and diseased CSF samples were reduced, alkylated, and each labeled with one of eight isobaric tagging reagents. After labeling, all eight samples were combined into a single pool and fractionated by cation exchange chromatography. The subsequent fractions were then analyzed by LC-MALDI on a 4800 MALDI TOF/TOF Analyzer. An analysis of the proteins identified in the CSF detailed several proteins that exhibited varying degrees of expression across the eight samples.