DO-MS

DO-MS optimizes liquid chromatography-tandem mass spectrometry (LC-MS/MS) acquisition and diagnostics for bottom-up and single-cell proteomics (including SCoPE-MS), enabling identification and resolution of factors that reduce MS2 ion sampling and signal intensity.

Key Features:

• Multi-level data integration: Integrates data across all levels of bottom-up LC-MS/MS analysis to provide comprehensive diagnostics.
• Interactive visualization techniques: Employs interactive visualization techniques to diagnose performance issues in LC-MS/MS workflows.
• Diagnostic scope: Diagnoses contributors to low MS2 signal including inadequate liquid chromatography separation, ionization inefficiencies, suboptimal elution apex targeting, ion transfer problems, and poor ion detection.
• Elution apex optimization: Facilitates targeted optimization of elution peak apex sampling to improve apex targeting and ion accumulation times.
• Performance gains: Enables increases in ion delivery for MS2 analysis of up to 370% through optimized apex sampling and enhanced ion accumulation.
• Single-cell proteomics compatibility: Applied to single-cell proteomics by mass spectrometry (SCoPE-MS) workflows as well as general bottom-up proteomics.
• Complementary to MaxQuant: Complements outputs from software such as MaxQuant by providing integrated visualization and diagnostics for LC-MS/MS data.

Scientific Applications:

• Single-cell proteomics (SCoPE-MS): Diagnose and optimize LC-MS/MS acquisition parameters to improve protein detection and quantification in SCoPE-MS experiments.
• LC-MS/MS method development: Identify and resolve chromatographic, ionization, and ion transfer issues during method optimization for bottom-up proteomics.
• MS2 ion sampling and signal enhancement: Improve apex sampling efficiency and ion accumulation to increase MS2 signal intensity and peptide identification rates.

Methodology:

Integrates bottom-up LC-MS/MS data and applies interactive visualization-driven diagnostics to identify causes of low MS2 signal and to optimize elution apex sampling and ion accumulation times.