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MALDI-TOF mass spectrometry


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Related Terms
  • Analyte, biomolecules, bioterrorism, biotoxins, desorption, detector, DNA analysis, drug development, food contamination, genomics, ionization, laser, lipid analysis, MALDI imaging team imaging computer system, MALDI Molecular ImagerT, MALDI-TOF mass analyzer, mass spectrometry, matrix, matrix-assisted laser desorption/ionization time-of-flight, microwave-assisted, MITICS, molecular weight, oligonucleotide, polydisperse polymer, prenatal, proteomics, protein marker, single nucleotide polymorphism, SNP, tumor marker.

  • General: Genes are referred to as the building blocks of life. They are located inside the cell and contain the instructions for making all the proteins in the body, thus controlling an organism's development and function. Proteins are organic compounds composed of amino acids, and the sequence of the amino acids in a protein is determined by the genes.
  • Deoxyribonucleic acid (DNA) is a long thread-like molecule made up of large numbers of nucleotides arranged in a double strand. Nucleotides are molecules composed of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Nitrogenous bases in DNA are of two types: purines such as adenine (A) and guanine (G), and pyrimidines such as cytosine (C) and thymine (T).
  • The sequence of bases in DNA serves as the carrier of genetic, or hereditary, information. Long strands of nucleotides form nucleic acids. RNA (ribonucleic acid) is a nucleic acid that helps in protein synthesis. RNA is formed under the direction of DNA, and both RNA and DNA play key roles in forming amino acids.
  • Mass spectrometry: Mass spectrometry (MS), an analytical technique used to measure the molecular mass of a sample, can identify the chemical composition of a compound within the sample. Molecular mass is the mass of a molecule relative to the mass of a standard atom, now 12C (the mass of one molecule of carbon taken as 12.000). MS can be used to analyze tissues or bodily fluids such as blood, saliva, or urine. MS is based on the chemical breakdown of a sample into charged ions, or particles, which are then separated based on their charge and mass. The separated particles are later identified using a detector.
  • MS has widespread applications and is used to identify proteins, peptides, and oligonucleotides, which are short segments of DNA or RNA. Identifying these components helps researchers discover previously unknown multifunctional proteins and identify new functions of known proteins. MS may also improve the understanding of drug metabolism, including the modification or degradation of a drug, which in turn informs the discovery of new drugs. In clinical settings, MS may be used to test the effectiveness of a drug in an individual, thereby determining the appropriate treatment. MS may also be used to analyze water quality and to check for food contamination. Identifying contaminants is the first step in finding possible prevention or treatment options for them.
  • MALDI-TOF mass spectrometry: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry is a soft ionization method used in mass spectrometry (MS). Soft ionization is a technique that introduces large molecules into the mass analyzer without completely breaking down their structure. Desorption is a phenomenon in which a substance is released from or through a surface. Ionization is the process of converting an atom or molecule into an ion with the addition or removal of charged particles such as electrons. MALDI is based on exposing sample molecules to a laser light to ionize them, which makes it easier to manipulate them than neutral molecules. This process in turn makes identification of the target compound in the sample possible.
  • MALDI has been successfully used to analyze proteins, peptides, oligonucleotides, and oligosaccharides, a type of carbohydrate. This process can increase the total mass of samples to be accurately analyzed.
  • MS was first demonstrated in 1913 in a series of cathode ray tube experiments. In general, MS involves the generation, separation, and detection of gas-phase ions. One of the limitations of MS is the need to convert the target molecules or atoms into gas-phase ions because electromagnetic forces can more easily manipulate the ions than the original target molecule. The need to convert the molecules to gas-phase ions has slowed the widespread use of mass spectrometric techniques in the biological sciences because the conversion usually results in severe decomposition of biological molecules.
  • MALDI-TOF MS, as practiced today, is based on a concept introduced in 1989 by Franz Hillenkamp and Michael Karas. Ionization of large molecules results in decomposition because they are fragile and easily broken. This fragility causes changes in the nature of the molecule, results in unwanted products, and leads to inaccurate results. The introduction of the MALDI-TOF MS technique has reduced the limitations caused by decomposition of large biomolecules. Consequently, the use of MS techniques is now becoming more routine and commonly practiced.

  • General: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry is a soft ionization method used in mass spectrometry (MS) to identify the chemical composition of a compound within a sample. The sample used for MS may include tissues or bodily fluids such as blood, saliva, or urine. Ionized molecules are easier to manipulate than neutral molecules, which makes identification of the target molecule in the sample possible.
  • MS is an analytical technique to measure the molecular mass of a sample using a mass spectrometer. A mass spectrometer creates charged particles, or ions, from molecules and analyzes those ions to provide information about the molecular weight and mass of the compound and its chemical structure. Ions are molecules that have lost one or more electrons, making them electrically charged. A mass spectrometer is divided into three distinct regions: the ionization source, the analyzer, and the detector.
  • Ionization source: The first step involves introducing the sample into the ionization source of the mass spectrometer. The method of sample introduction depends on the ionization method used and the type and complexity of the sample. The ionization method in turn depends on the type of sample and mass spectrometer. The ionization source ionizes, or gives electrical charge to, the sample molecules because ions are easier to manipulate than neutral molecules.
  • Some of the common ionization methods include matrix-assisted laser desorption ionization (MALDI), electrospray ionization (ESI), and fast atom bombardment (FAB). The process of ionization differs in each method. In MALDI, a laser is used to ionize the sample, whereas in FAB a high-energy beam of neutral atoms is used. In ESI, the sample solution containing the dissolved compound flows through a source chamber to form electrically charged droplets. Highly charged molecules are formed when the solvent in the solution vaporizes.
  • Mass analyzer: The ions then move into the analyzer region of the mass spectrometer, where the ions are separated according to their size and charge. There are a number of mass analyzers available, and some of them include time-of-flight (TOF) analyzers, which use an electric field to filter ions based on their size and charge. The compatibility of different analyzers varies with different ionization methods. For example, MALDI is generally used with a TOF analyzer because of its huge mass range and because it is more suitable for the MALDI ionization.
  • Detector: The detector in the mass spectrometer monitors and increases the ion current. There are many types of detectors, and most of them produce an electronic signal when struck by an ion. The signal is transmitted to the data system and is stored in the form of mass spectra. A mass spectrum is commonly presented as a vertical bar graph, in which each bar represents an ion having a specific mass-to-charge (m/z) ratio, with the amount of the ion indicated by the length of the bar. The m/z value of an ion is equivalent to mass itself because most of the ions formed in the mass spectrometer have a single charge. Hence, this method facilitates the accurate identification of the target molecule.
  • MALDI-TOF mass spectrometry: In MALDI-TOF mass spectrometry, a laser is used to ionize the sample of interest. The sample is premixed with a highly absorbing matrix compound to obtain consistent and reliable results by preventing decomposition of molecules. When the sample with matrix is bombarded with laser light, the matrix absorbs the laser energy and becomes charged. The charged matrix in turn transfers part of the charge to the target molecule (e.g., protein), thus giving a charge to the molecules. This facilitates efficient energy transfer and spares the molecules from excessive or disruptive direct energy and prevents them from breaking down.
  • The time-of-flight (TOF) analyzer is most commonly used with MALDI because of its large mass range and because it is suited to the MALDI ionization process. In the TOF analyzer, the ionized target molecules are accelerated using an electrical field. Different molecules are separated according to their size and charge and reach the detector at different times, each producing a distinct signal. Because all molecules break down into the same fragments, the same mass spectrum, known as a molecular fingerprint, is displayed. This allows for easy detection. MALDI-TOF is a very sensitive method that allows detection of very small quantities of molecules.
  • Interpretation of mass spectra: Various techniques are used to interpret the data obtained through this process. Generally, the unknown molecule is identified by comparing the mass spectrum obtained with a library of mass spectra that is already stored. If the molecule does not match any compound in the library, then a computer software assisted interpretation technique is used.
  • Some advancements have been made in conventional MALDI-TOF mass spectrometry, such as the MALDI Molecular ImagerT from Bruker Daltonics, Massachusetts. This imaging device provides high-resolution images, which makes identification easier than with conventional methods. Hence, MALDI imaging is a fast and reliable method for analysis of proteins, peptides, and other molecules taken from tissues.

  • General: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used in various studies to improve the existing method of MALDI-TOF MS, discover previously unknown multifunctional proteins, and identify new functions of already known proteins. MALDI-TOF MS is currently being tested in clinical trials in the field of drug development for protein biomarkers, which may help in developing disease therapy and predicting disease outcome.
  • Biomarkers help predict disease susceptibility, outcome, treatment response, and toxicity. For example, proteins and fats may be used as biomarkers, which may suggest why some smokers get cancer but others do not; why some people have a higher incidence of cancer after exposure to a toxicant and others do not; and why some women are more prone to breast cancer than others.
  • Heart: Researchers are conducting studies using MALDI-TOF MS to discover specific targets for a heart protein called S-nitrosylation, which has been associated with the development of several heart diseases. This discovery may help researchers understand the function of the protein and develop drugs against the pathway through which the protein causes disease.
  • Identification of biotoxins: MALDI-TOF MS has been used to identify the toxins produced by cyanobacteria (blue-green algae) that may cause poisoning in animals and humans. The algae bloom, also known as "red tide," may occur in lakes and drinking water reservoirs. The algae accumulate rapidly and form dense visible patches near the water surface, leading to the discoloration of water. Identification and characterization of the biotoxin helps to evaluate associated health risks and to develop therapies against it.
  • In July 2008 in the United States, the New Hampshire Department of Environmental Services issued an alert that people should avoid eating lobster tomalley because it had unsafe levels of red tide or paralytic shellfish poison. Tomalley is a soft, green substance found in the body cavity of lobsters. The symptoms of shellfish poisoning include tingling, burning, drowsiness, and incoherent speech. This condition may lead to death in some cases. This situation demonstrates the importance of identifying such biotoxins and taking certain precautions regarding food safety.
  • Detection of biological weapons: A bioterrorism attack is the deliberate release of viruses, bacteria, or other germs used to cause widespread illness or death in people, animals, or plants. Researchers have used MALDI-TOF MS to identify ricin, the toxic component of Ricinus communis (castor oil plant), which may be used as a biochemical weapon. Hence, MALDI-TOF MS has the potential to be used as a new tool for the detection of toxins used in bioterrorism.

  • General: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) is used to analyze molecules such as proteins, sugars, peptides, and oligonucleotides, which are short segments of DNA or RNA. MALDI-TOF MS is widely used in genomics and proteomics. Proteomics is the large-scale study of the structure and function of proteins. Genomics is the study of an organism's genome, the sum total of genetic information in an organism. MALDI-TOF MS is used to diagnose diseases. For example, MALDI-TOF MS is used to examine protein markers such as interleukin-6 for the detection of heart disease, to monitor disease states, and to determine medical treatments.
  • DNA analysis: MALDI-TOF MS has also been used to detect any sequence variation in the genome of an organism. This use has been helpful in identifying single nucleotide polymorphisms (SNPs), which are DNA sequence variations that occur when a single nucleotide in the genome sequence is altered. Nucleotides are the building blocks of DNA. SNPs may act as biological markers and thereby help to locate genes that are associated with disease. SNPs may also be used to track the inheritance of disease genes within families, which helps in evaluating an individual's risk of developing a disease.
  • Drug development: MALDI-TOF MS is especially useful in the development of new drugs that target particular proteins and pathways. This technique is used to analyze the structure and function of proteins, and may identify proteins associated with a disease. Using this information, drugs may be designed to interfere with the action of the protein, thereby targeting the disease. MALDI-TOF MS can also be used to improve existing drugs and to better understand individual drug response in terms of drug-body interactions (pharmacodynamics) and side effects.
  • Lipid analysis: MALDI-TOF MS has been used to analyze lipids such as high-density lipoproteins (HDL, or good cholesterol) and low-density lipoproteins (LDL, or bad cholesterol), which helps researchers and clinicians better understand atherosclerosis. Atherosclerosis is a condition in which plaque builds up inside the arteries that carry blood to the heart. This buildup, often caused by too much LDL or too little HDL, may lead to several heart diseases, and ultimately, death. Because MALDI-TOF MS rapidly provides a reliable profile of lipoproteins, it is used to analyze lipids. However, the method requires that a lipid separation be done previously in order to accurately detect the lipid oxidation products.
  • Protein biomarkers/tumor markers: MALDI-TOF MS has been used to discover novel protein biomarkers, which may help detect and diagnose disease, monitor the course of disease, and/or determine the disease stage. Tumor markers may be examined from very small samples of tissue, which creates new possibilities for monitoring cancer treatment and therapy. Some of the examples of protein biomarkers for heart disease include interleukin-6, interleukin-8, fibrinogen, and troponins. Biomarkers help predict disease susceptibility, outcome, treatment response, and toxicity. Markers can suggest why some smokers get cancer but others do not; why some people have a higher incidence of cancer after exposure to a toxic agent and others do not; and why some women are more prone to breast cancer than others.
  • Protein characterization: MALDI-TOF MS may be used to identify and analyze proteins and their interaction with other proteins, nucleic acids, enzymes, small molecules, and drugs for comparing normal states of health with those of disease states. MALDI-TOF MS may also be used for peptide mass fingerprinting, an analytical method used for protein identification. This method may help in understanding the impaired protein pathways; why abnormal proteins and chemicals are produced; and the proteins that need to be targeted for treatment of disease.

  • One major limitation associated with matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) is the difficulty in mass determination of large molecules. Also, in cases in which the mass difference between nucleotides is very small, MALDI-TOF may not be able to accurately determine the mass of such molecules.
  • Conventional MALDI-TOF MS has not been used much in quantitative studies, which involves the determination of the number of target molecules in a sample of interest, because of lack of standardization. Also, the conventional technique of MALDI-TOF MS requires the destruction of the specimen under study. However, with many advancements made to MALDI-TOF, the specimen may be preserved for further studies.


Future research
  • General: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used in various studies to improve the existing method of MALDI-TOF MS, to discover previously unknown multifunctional proteins, and to identify new functions of known proteins.
  • Microwave-assisted enzyme digestion: Researchers are conducting studies to develop a simplified and improved version of MALDI-TOF MS by using microwave-assisted digestion of enzymes and removal of proteins with extremely small particles called nanoparticles. This method will avoid the formation of peptide and oligosaccharide (carbohydrate) ions in MS analysis. Although initial results show promise, further studies are required to evaluate this method further.
  • MITICS (MALDI imaging team imaging computing system): Scientists have developed new software called MITICS for MALDI imaging, which helps to process the data collected using MALDI-TOF MS. MITICS also reconstructs images, making it possible to easily detect the compound of interest in the sample. The conventional technique of MALDI-TOF MS requires the destruction of the specimen under study, but this new technology preserves the integrity of the tissue and avoids multiple steps such as purification and separation.
  • Prenatal detection: MALDI-TOF mass spectrometry is currently being studied for use in prenatal detection of chromosomal abnormalities such as trisomy 21, also known as Down syndrome. Prenatal detection is the screening for diseases in a fetus. Trisomy 21 is caused by the presence of an extra chromosome and is characterized by impairment of physical growth and decreased cognitive and learning abilities.
  • Because MALDI-TOF can detect small differences in mass, even single nucleotide polymorphisms (SNPs) can be easily determined. SNPs are DNA sequence variations that occur when a single nucleotide in the genome sequence is altered. In addition, the technique has several advantages over other screening tests in current use: faster output and no dependence on prior cell culture.

Author information
  • This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (

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