The dilemma of: LC-MS or MALDI-TOF?

The dilemma of: LC-MS or MALDI-TOF?

Write By: rakesh Published In: The Dilemma Series Created Date: 2015-07-08 Hits: 5948 Comment: 0

With the advent of two major techniques within the past century, scientists are faced with a dilemma for their protein identification studies. Both the techniques fall under the umbrella of Mass Spectrometry, analyze protein samples and provide results in the form of m/z spectra. So, what’s the difference? Why and when should you choose any one technique over the other? Before we answer these questions, here’s a brief introduction to what these things mean.

Mass spectrometry began as a tool for structural elucidation (more so, confirmation) by physicists back in the 1980s. It has now metamorphosed into an indispensable tool for the biology community. The technique has now been combined with a variety of other applications such as GC-MS wherein substances separated by Gas Chromatography are analyzed by the mass spec analyzer. Among these, LC-MS and MALDI-TOF find popular uses in protein identification and quantification.

In LC-MS, proteins are subjected to digestion and the fragments are separated by HPLC and then directly analyzed within tandem mass spectrometers associated with the HPLC column generating multiple mass spectra for each fragmented peptide. These spectra are then analyzed using a database to identify the protein in the sample.

The MALDI-TOF technique is sometimes classified as protein fingerprinting. In this technique, the protein sample is subjected to proteolytic digestion by an enzyme such as trypsin and an MS spectrum (not spectra) is generated compiling the masses of all peptides which then act as fingerprints while performing the database search

.Principle of MALDI TOF


Listed below are features of both the techniques:

Features of MALDI-TOF:

Usually recommended when you are studying an organism with small genome size.

  • It is faster and convenient. The result can be obtained in minutes.
  • It is relatively inexpensive.
  • Requires very low sample amounts. High sensitivity.
  • Requires pure samples. Any contamination can hamper the quality of results.
  • Since a mass spectrum is generated for all peptides, analysis of complex mixtures is often not reliable.
  • For database search, extremely high homology is required.

Features of LC-MS:

  • High sensitivity and reliability.
  • Useful for analysis of a complex mixture of proteins.
  • Yields high confidence identification results due to sequence dependence of data obtained from tandem mass spectrometry.
  • For database search, extremely high homology is required.
  • Used for analysis of modifications such as phosphorylation, acetylation etc. 

You can now weigh the pros and cons of both the techniques and identify the ones most suitable to you.


1.       Inc, BioSynthesis. Tech Lounge: FAQ. 1964. 8 July 2015 <>.

2.       Inc., ProtTech. "ProtTech Inc." 2003-2011. 8 July 2015 <>.

3.       Medicine, Yale School of. Proteomics: Protein Identification. 2014. 8 July 2015 <>.

4.       Shaw, Gina. John Wiley & Sons Inc, Spectroscopy NOW. 2015. 8 July 2015 <>.

Tags: proteomics protein identification lc-ms mass spectrometry maldi maldi-tof chromatography proteins

Related Blogs By Tags

Leave A Comment