Utilizing peptide centric DIA on an Orbitrap Lumos and diaPASEF on a Bruker timsTOF Pro for Complex Proteomics Quantitation.

Data Independent Acquisition (DIA) is a relatively new and exciting method for quantitative proteomics. Unfortunately, it can be daunting and time consuming to optimize DIA acquisition and analysis in an academic core facility. In addition, there are several different competing platforms available a core facility can use to generate DIA data. Here we will compare several real-world proteomics samples using a peptide centric DIA method on a Thermo Lumos mass spectrometer and compare them to the relatively new diaPASEF acquisition method utilizing ion mobility on the relatively new Bruker timsTOF. Data quality, sensitivity, specificity, cv's, acquisitions speed, data analysis and software availability will all be compared with the lens of generating, processing and returning data to collaborators in an academic core facility.