Genome-scale proteome quantification by DEEP SEQ mass spectrometry.

Area of Science:

• Proteomics
• Mass Spectrometry
• Genomics

Background:

• DNA sequencing advances for personalized medicine contrast with lagging protein-level data generation.
• Current proteomics methods face limitations in depth, throughput, sample preparation, and experimental time.

Purpose of the Study:

• To bridge the gap between genomics and proteomics by developing an advanced protein analysis platform.
• To achieve genome-scale proteome coverage and accurate protein quantification.

Main Methods:

• Developed a novel approach using simple detergent lysis and single-enzyme digest.
• Employed orthogonal separation of peptides and nanoflow liquid chromatography-tandem mass spectrometry.
• Utilized an automated platform for efficient peptide sequencing and quantification.

Main Results:

• Achieved genome-scale proteome coverage comparable to RNA-seq ribosomal profiling.
• Provided accurate quantification for multiplexed isotope labels.
• Unambiguously quantified 11,352 gene products in murine stem cells, covering 70% of Swiss-Prot.

Conclusions:

• The developed mass spectrometry platform significantly advances deep and efficient proteome analysis.
• This approach enables capturing protein regulation across a wide dynamic range, complementing gene expression data.
• The platform holds promise for applications in personalized medicine and understanding biological transitions.