The Protein Profiling Group has two Waters Synapt G2-Si mass spectrometers coupled to nanoACQUITY ultra-performance LC systems. This configuration offers not only excellent sensitivity and quantification of proteins but also has the ability to handle hugely complex biological samples with high dynamic protein abundance range.
LC Systems: nanoACQUITY UPLC
The nanoACQUITY UPLC is a true direct nanoflow system, delivering highly resolved and reproducible chromatography from the very low volume samples produced in proteomics experiments. The nanoACQUITY UPLC systems are compatible with a wide range of nanoflow columns and the separations can be tailored to suit individual requirements.
Waters SYNAPT G2-Si mass spectrometry instruments
Two different methods are available in our instruments for peptide and protein identification: 1) MSe (data-independent analysis, DIA) where every detectable ion is fragmented (collision induced dissociation) and the data produced is recorded and aligned with the parent ions: 2) and DDA (data dependent analysis, DDA) which allows for the preselection of ions for a more targeted approach.
For both methods we use an additional separation technique which employs a T-Wave Ion Mobility cell. In this approach complex mixture are separated with the nanoACQUITY UPLC and then further separated in the Ion Mobility Cell on the basis of cross-sectional area of the peptides or fragments to yield (HD-MSe and HD-DDA spectra).
Collection of data in a DIA mode coupled with high resolution allows us to generate very accurate and reproducible label-free quantification of proteins in complex sample mixtures with a large dynamic range, thus reducing the necessity for expensive and difficult labelling techniques.