Aliquoting of isobaric labeling reagents for low concentration and single cell proteomics samples

Abstract

AbstractThe introduction of isobaric tagging reagents enabled more accurate, high-throughput quantitative proteomics by enabling multiple samples to be multiplexed. One drawback of these workflows is the relative expense of the proprietary isobaric reagents, which is often only second to the expense of the instruments themselves. These highly reactive chemical tags are only commercially available in relatively large aliquots compared to the typical amounts of peptides analyzed in proteomic workflows today. Excess reagents are typically disposed of following a single labeling experiment or those performed within a few days of opening a new kit. We present a simple procedure to aliquot commercial isobaric tagging reagents and demonstrate the successful and high efficiency labeling of multiple samples over a period of six months. The samples presented herein were selected as the most diverse ones labeled by prepared aliquots from a single labeling reagent kit over this period. We observe comparable labeling efficiency from 100 microgram to 100 picograms of peptide when labeling samples from both human digest standards, cancer cell lines prepared in-house and from cells directly obtained from human organ donors, despite differences in cell type, lysis, and digestion procedures. No labeling experiment of whole human proteomics samples achieved less than 92% labeling efficiency over this period. When preparing phosphoproteomic samples 6 months after the date of the aliquoting procedure, we observed a decrease in labeling efficiency to approximately 86%, indicating the end of the useful lifetime of aliquots prepared in this manner. Over this period, we have effectively reduced the reagent costs of each experiment to less than 10% of the predicted costs when following the manufacturer instructions for use and disposal. While aliquoting of reagents can be performed by hand, we provide a complete template for automatic aliquoting using an affordable liquid handling robot, including plans for 3D printing of two parts we have found useful for streamlining this procedure.Abstract Graphic