Sunday, 6 April 2014

SWATH-MS and next-generation targeted proteomics

For proteomics, two main LC-MS/MS strategies have been used thus far. They have in common that the sample proteins are converted by proteolysis into peptides, which are then separated by (capillary) liquid chromatography. They differ in the mass spectrometric method used.

The first and most widely used strategy is known as shotgun proteomics or discovery proteomics. For this method, the MS instrument is operated in data-dependent acquisition (DDA) mode, where fragment ion (MS2) spectra for selected precursor ions detectable in a survey (MS1) scan are generated (Figure 1 - Discovery workflow). The resulting fragment ion spectra are then assigned to their corresponding peptide sequences by sequence database searching (See Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective).

The second main strategy is referred to as targeted proteomics. There, the MS instrument is operated in selected reaction monitoring (SRM) (also called multiple reaction monitoring) mode (Figure 1 - Targeted Workflow). With this method, a sample is queried for the presence and quantity of a limited set of peptides that have to be specified prior to data acquisition. SRM does not require the explicit detection of the targeted precursors but proceeds by the acquisition, sequentially across the LC retention time domain, of predefined pairs of precursor and product ion masses, called transitions, several of which constitute a definitive assay for the detection of a peptide in a complex sample (See Targeted proteomics) .

Figure 1 - Discovery and Targeted proteomics workflows