TVT viewer

TVT viewer analyzes the Triple Knockout (TKO) standard to benchmark and quantify interference in isobaric multiplexed mass spectrometry experiments such as SPS-MS3.

Key Features:

• Automated database searching: Automates database searching of the Triple Knockout (TKO) standard to identify peptides and proteins.
• Figures of merit: Reports traditional metrics including peptide and protein counts.
• Scan-specific ion accumulation times: Extracts and reports scan-specific ion accumulation times from mass spectrometry data.
• Interference-Free Index (IFI): Calculates the Interference-Free Index (IFI) to quantify the level of interference-free ions in the TKO standard.
• Pairwise TKO comparisons: Compares results between two TKO standards to evaluate differences between experimental conditions.

Scientific Applications:

• Interference benchmarking: Quantifies and benchmarks interference levels in isobaric multiplexing workflows such as SPS-MS3.
• Protocol optimization: Evaluates experimental parameters including stationary phase resin selection, MS2 isolation window width, and the number of synchronous precursor selection (SPS) ions.
• Instrument performance assessment: Compares TKO results over time or between setups to assess instrument performance and support troubleshooting.

Methodology:

Performs automated database searching of the TKO standard, reports peptide/protein counts and scan-specific ion accumulation times, calculates the Interference-Free Index (IFI), and plots/comparatively analyzes results from different TKO standards.