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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 proteomics...

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Updated: Jun 25, 2026

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

Published on: June 6, 2022

Quantitative phospho-proteomics based on soluble nanopolymers.

Anton Iliuk¹, W Andy Tao

¹Department of Biochemistry, Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.

Methods in Molecular Biology (Clifton, N.J.)

|February 26, 2009

Summary

This summary is machine-generated.

This study introduces two nanopolymer-based methods for enriching phosphopeptides, crucial for understanding cell signaling in diseases like cancer and diabetes. These techniques improve phosphoprotein identification and mapping in mass spectrometry-based proteomics.

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Last Updated: Jun 25, 2026

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

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Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Published on: October 12, 2009

Area of Science:

Proteomics
Biochemistry
Molecular Biology

Background:

Phospho-proteomics globally analyzes protein phosphorylation, vital for disease research (cancer, diabetes).
Mass spectrometry is key for protein phosphorylation profiling.
Sub-stoichiometric phosphorylation presents challenges in phosphoprotein and phosphosite identification.

Purpose of the Study:

To present two novel nanopolymer-based methods for effective phosphopeptide enrichment.
To overcome challenges in mass spectrometry-based phospho-proteomics.
To enable reproducible and efficient quantitative phospho-proteomics.

Main Methods:

Method 1: Reversible phosphoramidate bond formation between nanopolymers and phosphopeptides for size-based filtering.
Method 2: Selective chelation of phosphopeptides to functionalized nanopolymers (zirconia/titania) using hydrazide chemistry for solid-phase isolation.
Integration with stable isotope labeling for quantitative analysis.

Main Results:

Demonstrated robust phosphopeptide enrichment using both nanopolymer strategies.
Achieved selective isolation of phosphopeptides from complex mixtures.
Enabled reproducible and efficient quantitative phospho-proteomics.

Conclusions:

The presented nanopolymer-based methods offer effective solutions for phosphopeptide enrichment.
These strategies enhance the identification and mapping of phosphosites in complex samples.
The methods facilitate advancements in understanding disease mechanisms through quantitative phospho-proteomics.