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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Related Experiment Video

Updated: Jun 24, 2025

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier

Published on: December 9, 2022

Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples.

Marion Pang¹, Jeff J Jones^1,2, Ting-Yu Wang^1,2

¹Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States.

Journal of Proteome Research

|June 4, 2024

Summary

This summary is machine-generated.

Using a monosubstrate protease in single-cell proteomics improves quantitative accuracy and proteome coverage. This approach enhances the identification of low-abundance proteins in limited samples, advancing single-cell analysis.

Keywords:

bottom-up proteomics peptide identification optimization protease choice single-cell proteomics

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Area of Science:

Mass spectrometry
Proteomics
Biochemistry

Background:

Sophisticated mass spectrometry enables deep proteome exploration, requiring a balance between quantitative precision and analyte detection.
Oversampling abundant proteins in bottom-up proteomics limits identification of unique and low-abundance proteins, particularly in limited samples like single cells.
Existing methods like depletion and fractionation are suboptimal for single-cell samples, highlighting the need for improved proteomic workflows.

Purpose of the Study:

To investigate the use of a monosubstrate protease for single-cell proteomic analysis.
To assess the impact of monosubstrate protease on quantitative accuracy and proteome coverage compared to trypsin.
To address the challenge of analyte complexity in single-cell proteomics.

Main Methods:

Proteomic analysis of single-cell equivalent digest samples.
Enzymatic digestion using a monosubstrate protease.
Comparison with trypsin digestion for quantitative accuracy and proteome coverage.

Main Results:

A monosubstrate protease improved quantitative accuracy in single-cell equivalent samples.
High proteome coverage, comparable to trypsin, was maintained.
The method shows promise for enhancing the analysis of limited samples, including low-abundance proteins.

Conclusions:

Monosubstrate protease digestion is a viable strategy to improve quantitative accuracy in single-cell proteomics.
This approach helps overcome limitations associated with analyte complexity in minute biological samples.
Future single-cell proteomic workflows should consider enzyme kinetics and analyte complexity for optimized experimental design.