Miniprep assisted proteomics (MAP) for rapid proteomics sample preparation.

Area of Science:

• Biochemistry
• Analytical Chemistry
• Proteomics

Background:

• Detergents improve protein digestion for proteomics but interfere with mass spectrometry.
• Filter-based methods remove detergents but can be costly.
• Novel, cost-effective sample preparation is needed for enhanced proteomics.

Purpose of the Study:

• To investigate the use of low-cost DNA purification spin-filters (Minipreps) for protein binding and digestion.
• To develop and validate a new proteomics sample preparation method named Miniprep Assisted Proteomics (MAP).
• To assess MAP's efficiency, reproducibility, and cost-effectiveness compared to existing techniques.

Main Methods:

• Proteins were bound to silica-based filters (Minipreps) with lyotropic salts.
• On-filter protein digestion was performed.
• Nano UHPLC-MS/MS was used for proteome profiling and quantitative analysis.
• MAP performance was benchmarked against commercial trapping methods using *Escherichia coli* lysates.

Main Results:

• MAP demonstrated equivalent or greater protein yields compared to commercial methods across various sample amounts.
• Proteome profiling of *E. coli* lysates showed 99.3% overlap with existing approaches.
• High reproducibility was achieved, with 98.8% protein-level reproducibility at 1% FDR.
• Label-free quantitative proteomics revealed 91.2% of quantified proteins had a coefficient of variation <20%.

Conclusions:

• Miniprep Assisted Proteomics (MAP) is an efficient, ultra-low-cost sample preparation technique.
• MAP offers high protein recovery, depth, and reproducibility suitable for bottom-up proteomics.
• The method utilizes commercially available devices, making it an accessible alternative for proteomics research.