Gel electrophoresis is an important methodology employed for protein analysis, which contains many different techniques, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing (IEF), and so on. SDS-PAGE, the most commonly gel electrophoresis used for proteins, provides an easy method to estimate the molecular weight of proteins, assess the complexity of the sample or the purity of a preparation, and monitor the fractions obtained during chromatographic or other purification procedures. Moreover, electrophoretic patterns are required by ICH Q6B for the analysis of biopharmaceuticals.

By removing most of the proteins in biological samples, body fluids and tissue extracts, with size exclusion chromatography,

Currently two peptidomic approaches for biomarker discovery are under investigation:

Peptidomics studies can provide a wealth of information about disease states, drug efficacy or toxicity.

Peptidomics studies can provide a wealth of information about disease states, drug efficacy or toxicity.

Peptidomics studies can provide a wealth of information about disease states, drug efficacy or toxicity.

The application of Bottom-Up strategy is limited by incomplete or ambiguous characterization of alternative splice forms, diverse modifications and endogenous protein cleavages. As an alternative, the Top-Down strategy has been utilized more with the advancement of analytical instruments. Except for FT-ICR mass spectrometer, invention and innovation of orbitrap mass spectrometer has promote the development of top-down proteomics.

In top-down proteomics, intact protein molecular ions generated by ESI or MALDI are introduced into mass analyzer and are subjected to gas-phase fragmentation. Top-down analysis facilitates direct observation of C- and N-termini for identification of truncations and distinguish one isoform from the other by different sequences.

Currently, there are two major types of approaches to protein biomarker discovery: top-down and bottom-up proteomics.

Although SUMO has very little sequence identity with ubiquitin at the amino acid sequence, it has a nearly identical structural fold.