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Protein Digestion

Protein Digestion

Protein digestion begins in the stomach, where the highly acidic environment can easily disrupt protein structure by exposing the peptide bonds of polypeptide chains. After polypeptide chains are broken into individual amino acids by a series of digestive enzymes, the amino acids are transported to the liver via the bloodstream to produce energy.

The Proteasome

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
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Peptide Identification Using Tandem Mass Spectrometry

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Updated: Mar 9, 2026

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

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Published on: April 28, 2022

ArgC-Like Digestion: Complementary or Alternative to Tryptic Digestion?

Vahid Golghalyani¹, Moritz Neupärtl¹, Ilka Wittig^2,3,4

¹Institute of Pharmaceutical Chemistry, Goethe-University , Frankfurt am Main 60438, Germany.

Journal of Proteome Research

|January 5, 2017

Summary

Chemically modifying lysine residues in proteins allows trypsin to mimic ArgC digestion, enhancing protein identification. This improved method offers a superior alternative to conventional trypsin digestion for proteomics.

Keywords:

ArgC acetylation amino modification carbethoxylation on bead digestion propionylation protein modification reductive methylation shotgun proteomics trypsin

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Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

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Published on: July 19, 2019

Area of Science:

Proteomics
Analytical Chemistry
Biochemistry

Background:

Enzymatic digestion using multiple proteases enhances protein identification in bottom-up proteomics.
Combining trypsin with ArgC can improve sequence coverage but is limited by ArgC's low selectivity.

Purpose of the Study:

To develop a method mimicking ArgC digestion by chemically modifying lysine residues.
To evaluate amine modifications for enhancing trypsin's specificity towards arginine.

Main Methods:

Chemical modification of lysine residues using dimethylation, acetylation, propionylation, and carbethoxylation.
Optimization of modification protocols to achieve near-complete conversion of primary amines.
Tryptic digestion of Escherichia coli lysate proteins after lysine modification.

Main Results:

All tested amine modifications achieved nearly complete conversion of primary amines.
Propionylation resulted in the identification of 9216 unique peptides and 1439 proteins.
This approach identified 150 additional proteins compared to conventional trypsin digestion, reducing sample complexity and improving fragmentation.

Conclusions:

Chemical modification of lysine residues creates a viable and superior alternative to conventional trypsin digestion.
Arg-C like digestion, achieved through lysine modification, should be considered a primary method, not just complementary.
This strategy significantly enhances protein identification efficiency in complex samples.