Mass Spectrometry

The main instruments needed for the analytical pipeline are powerful high-end mass spectrometers with high sensitivity, accuracy and resolution:

5 high resolution mass spectrometers, all fitted with high pressure nano-capillary HPLCs

• Q Exactive plus MS with Easy-nLC 1000 system
• Q Exactive plus MS with Ultimate 3000 LC system
• Q Exactive HFX MS with Ultimate 3000 LC system
• Exploris 480 MS with Evosep one LC system
• Exploris 480 MS with Vanquish neo LC system

Data-Independent Acquisition (DIA) and Data-Dependent Acquisition (DDA) are two fundamental approaches in mass spectrometry-based proteomics. Both methods aim to identify and quantify proteins in complex samples, but they differ significantly in their methodologies and outputs. DDA (Data-Dependent Acquisition) selects specific peptide ions for fragmentation based on their intensity in a survey scan. Typically selects the most abundant precursor ions for MS/MS analysis. DIA (Data-Independent Acquisition) fragments all peptide ions within a defined mass-to-charge (m/z) window, thus offers more comprehensive coverage and better reproducibility but with more complex data analysis. The choice between DDA and DIA depends on the specific research question, sample complexity, and desired outcomes of the proteomics study.