Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification with a...

Area of Science:

• Proteomics
• Analytical Chemistry
• Biotechnology

Background:

• Proteomic workflows are typically discovery-based or targeted, using different instrumentation.
• High-resolution analyzers are common for discovery, while triple quadrupoles excel in targeted workflows.
• Recent advances show quadrupole-ion trap instruments offer superior targeted performance.

Purpose of the Study:

• To expand the capabilities of a quadrupole-ion trap platform for multiplexed shotgun proteomics.
• To introduce and evaluate ion-trap multiplexed tandem mass spectrometry (iTMTproC) for quantitative proteomics.
• To benchmark iTMTproC against established methods like MultiNotch MS³.

Main Methods:

• Utilized a quadrupole-ion trap instrument (Stellar MS) for iTMTproC.
• Performed benchmarking experiments with defined standards.
• Validated the approach using a developmental time-series analysis of frog embryos.

Main Results:

• iTMTproC demonstrated quantification accuracy and interference reduction comparable to MultiNotch MS³.
• iTMTproC quantified slightly more proteins than MultiNotch MS³.
• Proteomic data from iTMTproC in frog embryos closely matched MultiNotch MS³ results, with increased protein depth.

Conclusions:

• Quadrupole-ion trap systems are versatile for highly accurate, multiplexed quantitative shotgun proteomics.
• iTMTproC provides a cost-effective alternative for advanced proteomic analyses.
• This extends the functionality of targeted instrumentation for broader proteomic applications.