Can All Pulled-Down Proteins Be Reliably Identified by Mass Spectrometry?

Not all proteins isolated via pull-down assays can be successfully identified by mass spectrometry. The outcome of protein identification depends on several key factors:

 

Protein Abundance

Highly abundant proteins are more readily detected, whereas low-abundance proteins may fall below the detection threshold of the mass spectrometer.

 

Sample Preparation Quality

Protein loss can occur during sample handling, particularly for proteins that are prone to degradation or susceptible to nonspecific adsorption to tube surfaces.

 

Sensitivity of the Mass Spectrometry Platform

The detection limit is directly influenced by the sensitivity of the instrument, which defines the minimum protein quantity required for reliable identification.

 

Consequently, if a pull-down experiment enriches a low-abundance protein that is partially lost during processing, the protein may remain undetected even when analyzed using a high-sensitivity mass spectrometry system—especially in complex biological matrices such as cell lysates.

 

MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.

Related Services

Pull Down based Protein Analysis Service with Mass Spectrometry