Basis of differentiation 

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SDS-PAGE

Definition 

Is a laboratory technique that separates proteins based on their 3D conformation (size, shape, and charge)

Is a laboratory technique that separates proteins based on their molecular weight or mass

Gel feature

Uses non-denaturing gel 

Uses denaturing gel 

Presence of SDS in Gel

SDS is absent

SDS is present as a detergent to impart a negative charge on the sample 

Separation criteria

Proteins are separated based on molecular size and overall charge

Proteins are separated based on molecular weight

Sample preparation

Protein samples are not heated

Protein samples are heated

Buffer composition

Reducing agent is not present in the buffer

Buffer has a reducing agent such as BME or DTT 

Temperature

Is run at 40°C

Is run at room temperature

Net charge on proteins

May be either positive or negative

Is always negative

State of protein

Native conformation or folded state

Denatured

Protein stability

High stability 

Low stability

Recovery of original protein

Can be recovered after separation

Cannot be recovered after separation as it is denatured during the process

Protein function

Proteins retain their function

Proteins lose their function

Ease of use

Comparatively difficult resulting in infrequent usage

Easier to perform and is used frequently 

Applications

Is used to:

• Purify proteins from a mixture in native form
• Study protein structure, function, and subunit composition 

Is used to:

• Detect presence of a protein
• Check protein expression
• Determine molecular weight (MW) of a protein