Mass spectrometry of proteins - applications in proteomics

Mass spectrometry has become in recent years an increasingly important tool in the field of proteomics. Traditionally, protein biochemists tend to study the structure and function of individual proteins. Proteomics researchers, in contrast, want to learn more about how large numbers of proteins in a living system interact with each other, and how they respond to changes in the state of the organism. One very important subfield of proteomics is the search for protein biomarkers for human disease. These can be proteins which are present in greater quantities in a sick person than in a healthy person, and their detection and identification can provide medical researchers with valuable information about possible causes or treatments. Detection in a healthy person of a known biomarker for a disease such as diabetes or cancer could also provide doctors with an early warning that the patient may be especially susceptible, so that preventive measures could be taken to prevent or delay onset of the disease.

New developments in MS technology have made it easier to detect and identify proteins that are present in very small quantities in biological samples. Mass spectrometrists who study proteins often use instrumentation that is somewhat different from the electron-ionization, magnetic deflection system described earlier. When proteins are being analyzed, the object is often to ionize the proteins without causing fragmentation, so 'softer' ionization methods are required. In one such method, called electrospray ionization, the protein sample, in solution, is sprayed into a tube and the molecules are induced by an electric field to pick up extra protons from the solvent. Another common 'soft ionization' method is 'matrix-assisted laser desorption ionization' (MALDI). Here, the protein sample is adsorbed onto a solid matrix, and protonation is achieved with a laser.

Typically, both electrospray ionization and MALDI are used in conjunction with a time-of-flight (TOF) mass analyzer component.

The ionized proteins are accelerated by an electrode through a column, and separation is achieved because lighter ions travel at greater velocity than heavier ions with the same overall charge. In this way, the many proteins in a complex biological sample (such as blood plasma, urine, etc.) can be separated and their individual masses determined very accurately. Modern protein MS is extremely sensitive – very recently, scientists were even able to obtain a mass spectrum of Tyrannosaurus rex protein from fossilized bone! (Science 2007, 316, 277).

In one recent study, MALDI-TOF mass spectrometry was used to compare fluid samples from lung transplant recipients who had suffered from tissue rejection to control samples from recipients who had not suffered rejection. Three peptides (short proteins) were found to be present at elevated levels specifically in the tissue rejection samples. It is hoped that these peptides might serve as biomarkers to identify patients who are at increased risk of rejecting their transplanted lungs (Proteomics 2005, 5, 1705).