Targeted mass spectrometry

Targeted mass spectrometry (also known as data-dependent mass spectrometry) is a technique of instructing the mass spectrometer to perform MSn (n=2 or 3) analysis on ions of specific m/z ratio, at specific time. The values of the m/z ratio and time are normally pre-defined in an inclusion list which is derived from previous MS analysis.

Targeted analysis allows the scientist to thoroughly analyze all ions, at all abundance range above the grass level, at any time window in the experiment. In contrast, non-targeted analysis would, typically, only allow the scientist to pick up the most abundant 50-100 ions over the entire experiment time. Such limitation of non-targeted analysis makes it less suitable for analyzing highly complex, highly dynamic sample such as human blood serum. Targeted mass spectrometry is becoming widely used in academia and in pharmaceutical and biotechnology industries for sensitive and quantitative detection of proteins, peptides and post-translational modifications.

However, the methods of utilizing targeted mass spectrometry are still at very primitive stage, in the sense that the inclusion list used in the targeted analysis is typically manually typed-in by scientists. In addition to that, only one inclusion list is allowed for the entire experiment. Such manual process is both labor-intensive and error-prone. This is largely due to the lack of a programmatic software API to the control unit of the mass spectrometer.

There has been some efforts in automating the generation of inclusion lists through the solution of external software. In 2010, Wu et al introduced a semi-automatic method in an effort of identifying low-abundance glyco-peptide. They implemented the automation through iterative experiments and their open-source software GLYPID. With minor modification, this approach can used in analyzing any other simple or complex samples. In addition to the advantage mentioned before, this semi-automated approach also saves substantial amount of time and efforts for scientists in manually picking ions and re-calibrating instruments.

Hopefully, with the release of a mature software API to the mass spectrometer, a fully automated solution would emerge in order to exploit the full potential of targeted analysis.