Enhancing Data Reliability in TOMAHAQ for Large ‐Scale Protein Quantification

AbstractThe analytical scale of most mass ‐spectrometry‐based targeted proteomics assays is usually limited by assay performance and instrument utilization. A recently introduced method, called triggered by offset, multiplexed, accurate mass, high resolution, and absolute quantitation (TOMAHAQ), combines both peptide and sample multiple xing to simultaneously improve analytical scale and quantitative performance. In the present work, critical technical requirements and data analysis considerations for successful implementation of the TOMAHAQ technique based on the study of a total of 185 target peptides across over 200 clinical pla sma samples are discussed. Importantly, it is observed that significant interference originate from the TMTzero reporter ion used for the synthetic trigger peptides. This interference is not expected because only TMT10plex reporter ions from the target peptides should be observed under typical TOMAH AQ conditions. In order to unlock the great promise of the technique for high throughput quantification, here a post‐acquisition data correction strategy to deconvolute the reporter ion superposition and recover reliable data is proposed.

Source: Proteomics - June 2, 2020 Category: Biochemistry Authors: Fang Liu, Kratika Singhal, Rowan Matney, Swati Acharya, Cezmi A. Akdis, Kari C. Nadeau, Allis S. Chien, Ryan D. Leib Tags: Technical Brief Source Type: research