The analytical scale of most mass spectrometry (MS)-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 multiplexing to simultaneously improve analytical scale and quantitative performance. In the present work we discuss critical technical requirements and data analysis considerations for successful implementation of the TOMAHAQ technique based on our study of a total of 185 target peptides across over 200 clinical plasma samples. Importantly, we observed significant interference originating 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 TOMAHAQ conditions. In order to unlock the great promise of the technique for high throughput quantification, here we propose a post-acquisition data correction strategy to deconvolute the reporter ion superposition and recover reliable data. This article is protected by copyright. All rights reserved.
View details for DOI 10.1002/pmic.201900105
View details for PubMedID 32032464