Two-dimensional database of mouse liver proteins. An update

Area of Science:

• Proteomics
• Biochemistry
• Molecular Biology

Background:

• Two-dimensional electrophoresis (2DE) is a powerful technique for protein separation.
• Mass spectrometry (MS) enables protein identification based on peptide mass fingerprinting.
• Comprehensive protein databases are crucial for understanding cellular functions.

Purpose of the Study:

• To update and expand the two-dimensional protein database for mouse liver.
• To identify novel mouse liver proteins and their gene products.
• To assess the utility of subcellular fractionation in protein discovery.

Main Methods:

• Proteins from male mouse liver microsomal and cytosolic fractions were separated using 2DE.
• Protein identification was performed using Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS).
• Peptide mass fingerprinting was employed, matching experimental data against theoretical masses of known proteins.

Main Results:

• Analysis of ~5800 spots from 14 gels identified ~2500 proteins from 328 genes.
• 112 newly identified gene products were added to the database.
• Fractionation was essential, with 55% of new proteins found in the microsomal fraction and 35% in the cytosolic fraction.
• Commonly identified proteins included heat shock proteins, housekeeping enzymes (e.g., ATP synthase), and structural proteins (e.g., tropomyosin).
• Most proteins were detected multiple times, with an average of 18-20 spots per gene product.

Conclusions:

• The updated mouse liver protein database provides a more comprehensive resource for researchers.
• Subcellular fractionation significantly aids in the discovery of novel proteins.
• The identified proteins represent key cellular components involved in various liver functions.