TomahaqCompanion

TomahaqCompanion facilitates creation of methods and analysis of data for the Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) targeted proteomics technique.

Key Features:

• Method development workflow: Generates priming run target lists, analyzes priming run data to refine targets, and creates TOMAHAQ method files.
• Data analysis and export: Performs quantitative analysis of TOMAHAQ data and exports quantitative results for downstream processing.
• Method parameter testing: Supports testing of parameters including the number of Selected Precursor Scans (SPS) notches and run length.
• Sensitivity and demonstration dataset: Reports limits of quantification of approximately 10–200 attomol in complex backgrounds demonstrated with an interference sample containing heavy yeast peptides, standard human peptide mixtures, TMT11-plex, and super heavy TMT (shTMT) isobaric labels.
• TOMAHAQ acquisition features: Implements peptide and sample multiplexing, multiple MS^n scans, mass inclusion lists, and data-driven filters consistent with the TOMAHAQ data collection scheme.

Scientific Applications:

• Targeted proteomics quantification: Enables sensitive and accurate quantification of peptides and proteins in multiplexed samples.
• Protein expression profiling: Supports comparative protein expression profiling across multiplexed experimental conditions.
• Biomarker discovery and validation: Applicable to biomarker discovery and validation workflows requiring precise targeted quantification.

Methodology:

Generation of priming run target lists, analysis of priming run data to refine targets, creation and export of TOMAHAQ method files, use of mass inclusion lists and data-driven filters, and handling of peptide/sample multiplexing with multiple MS^n scans; parameter testing includes Selected Precursor Scans (SPS) notches and run length.