timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein...

Area of Science:

• Proteomics
• Biomarker Discovery
• Mass Spectrometry

Background:

• Plasma proteome profiling is crucial for disease biomarker discovery.
• High variability in protein concentrations and technical challenges hinder deep protein quantitation.
• Advanced mass spectrometry techniques are needed to overcome these limitations.

Purpose of the Study:

• To evaluate the performance of timsTOF HT and timsTOF Pro 2 mass spectrometers for plasma proteome analysis.
• To compare neat plasma versus Proteograph-processed plasma for deep proteomics.
• To assess the impact of different liquid chromatography (LC) gradients and peptide loading masses.

Main Methods:

• Analysis of neat and Proteograph-processed plasma samples using timsTOF HT and timsTOF Pro 2.
• Evaluation across various peptide loading masses and LC gradients.
• Exploratory analysis of lung cancer patient plasma samples.

Main Results:

• timsTOF HT identified up to 76% more plasma peptide precursors and >2-fold more quantifiable precursors (CV < 20%) than timsTOF Pro 2.
• Proteograph processing increased detected peptide precursors by ~4.5 fold for both instruments compared to neat plasma.
• timsTOF HT showed ~50% increase in total and statistically significant peptide precursors in cancer vs. control samples.

Conclusions:

• timsTOF HT demonstrates superior performance for identifying and quantifying differences in diverse biological samples.
• The findings support improved disease biomarker discovery in large cohort studies.
• The study provides valuable datasets for optimizing LC-MS workflows in plasma proteomics.