Techniques and Applications of Protein Mass Spectrometry
Journal of Proteomics & Bioinformatics

Journal of Proteomics & Bioinformatics
Open Access

ISSN: 0974-276X

Commentry - (2021)Volume 14, Issue 9

Techniques and Applications of Protein Mass Spectrometry

Iman P. Maksum*
*Correspondence: Iman P. Maksum, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM.21, Raya Jatinangor, Indonesia, Email:

Author info »


Protein mass spectrometry is the study of proteins using mass spectrometry. For the precise mass measurement and characterisation of proteins, mass spectrometry is an essential technique, and a range of methodologies and apparatus have been developed for its various applications. Its uses include identifying proteins and their post-translational modifications, deciphering protein complexes, their components, and functional connections, and measuring proteins globally in proteomics. It may also be used to determine the interactions between different proteins and membrane lipids, as well as to localise proteins to distinct organelles.

Electrospray ionisation and matrix-assisted laser desorption or ionisation is the two most used techniques for ionising proteins in mass spectrometry. These ionisation methods are utilised in tandem mass spectrometry and other mass analyzers. In general, proteins are examined using either a "top-down" method, in which they are analysed whole, or a "bottom-up" approach, in which they are digested into fragments first. It's also possible to employ a "middle-down" method, in which bigger peptide fragments are examined.


Protein mass spectrometry demands that proteins in solution or solid form be ionised in the gas phase before being injected and accelerated in an electric or magnetic field for analysis. Electrospray Ionisation (ESI) and matrix-assisted laser desorption/ionization are the two most used techniques for ionising proteins. Electrospray allows delicate molecules to be ionised whole, sometimes retaining non-covalent connections, since the ions are generated from proteins in solution. In MALDI, proteins are placed in a matrix that is typically solid, and ions are generated by laser light pulses. Electrospray generates more multiply-charged ions than MALDI, allowing for higher mass protein measurement and better fragmentation for identification, whereas MALDI is faster and less susceptible to contamination, buffers, and additives.

Time-Of-Flight Mass Spectrometry (TOF MS) or Fourier Transform Ion Cyclotron Resonance (FT-ICR) are the most used methods for determining whole-protein mass. Because of their large mass ranges and, in the case of the FT-ICR, excellent mass accuracy, these two types of instruments are preferred here. When a protein is electrospray ionised, numerous charged species with a mass of 800 m/z 2000 are generated, and the resulting spectrum may be deconvoluted to estimate the protein's average mass to within 50 ppm or better using TOF or ion-trap equipment. Mass analysis of proteolytic peptides is a common approach of protein characterisation because it allows for the use of less expensive instrument designs. Furthermore, after entire proteins have been digested into smaller peptide fragments, sample preparation becomes easier. The MALDI-TOF devices are the most frequently used equipment for peptide mass analysis because they allow for rapid collection of peptide mass signatures. Tandem mass spectrometry is used to quickly and accurately analyse fragmentation spectra and identify proteins. Collision-induced dissociation is a technique that generates a collection of fragments from a single peptide ion in everyday applications.


MS may be used to detect proteins in two ways. Peptide mass finger printing searches a database of anticipated masses that would result from digestion of a list of known proteins using the masses of proteolytic peptides as input. If a protein sequence from the reference list produces a large number of projected masses that match the experimental values, there's a good chance it was present in the original sample. As a result, the peptide mass fingerprinting approach's throughput is limited by purification procedures. Peptides can also be fragmented with MS/MS for a more definite identification. The introduction of MALDI and ESI in the 1980s popularised the use of mass spectrometry to investigate proteins. These ionisation methods have been crucial in the identification of proteins. Franz Hillenkamp and Michael Karas developed the term "matrixassisted laser desorption ionisation" in the late 1980s. Hillenkamp, Karas, and their colleagues were able to ionise alanine by combining it with tryptophan and exposing it to a pulse 266 nm laser. The breakthrough, however significant, did not occur until 1987.

Author Info

Iman P. Maksum*
Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM.21, Raya Jatinangor, Indonesia

Citation: Maksum IP (2021) Techniques and Applications of Protein Mass Spectrometry. J Proteomics Bioinform.14:550.

Received: 08-Sep-2021 Accepted: 22-Sep-2021 Published: 29-Sep-2021 , DOI: 10.35248/0974-276X.21.14.550

Copyright: © 2021 Maksum IP. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.