Comparative analysis of DDA- and DIA-PASEF methods for proteomics analysis of human valve interstitial cells and osteoblasts during osteogenic differentiation

Shotgun proteomics is one of the key "omics" methods, the methodology of which is rapidly developing. Mass spectrometers of the TimsToF series (Bruker) with ion mobility are one of the young technological platforms for shotgun proteomics in which both data dependent (DDA) and data independent acquisition (DIA) proteomics methods might be performed. However, only a few comparisons of the effectiveness of DDA and DIA proteomics on TimsToF have been published, carried out mainly on the test samples. From the other hand, peculiarities of osteogenic differentiation of human valve interstitial cells (VICs) are fruitful therapeutic target for calcific aortic valve disease (CAVD) treatment. Still, there is no data whether pathological osteogenic differentiation of VICs similar to normal ossification. Combining this technical and biological tasks we performed comparative proteomics analysis of osteogenic differentiation of human VICs and osteoblasts by DIA- and DDA-PASEF proteomics on TimsToF Pro.