Mass spectrometry, mostly used in discovery-based proteomics, can also be applied to specifically analyze target proteins of interest. In the most mature technology for targeted analysis, known as selected (or multiple) reaction monitoring, a mass spectrometer called a triple quadrupole is programmed to detect specific peptides that uniquely represent proteins of interest, allowing researchers to quantitatively monitor these proteins with high sensitivity and reproducibility.
Mass spectrometry has an advantage over antibodies in that developing a new targeted assay is much faster than generating a new antibody, and issues of detection specificity (that is, antibody cross-reactivity) are greatly minimized. Antibodies still have the upper hand in terms of sensitivity of detection for low-abundance proteins. But a highly positive trait of mass spectrometry is its inherent ability to unambiguously detect multiple proteins in one experiment, allowing, for example, a systems biology researcher to look at what happens to protein levels upon perturbation of a protein network or a clinical researcher to measure how a panel of proposed biomarkers changes in a disease state.
An old technology made new
The triple quadrupole mass spectrometer (QQQ) was developed more than 30 years ago for small-molecule analysis. It operates as a dual mass filter that allows molecular ions of predetermined masses to be selected for fragmentation in the instrument. In recent years the use of the QQQ for targeted proteomics applications has escalated as methodological advances have made the technology more widespread.
Allison Doerr, Nature Methods, 10, 23, (2013)