Abstract: dia PASEF (Meier et al 2020) takes advantage of the additional dimension of separation provided by trapped ion mobility for the analysis of complex proteomics samples by data independent analysis (DIA). Additionally TIMS separation increases selectivity, excludes singly charged precursors from fragmentation and cleans up the sample by concentrating signals from noise. Making use of the correlation of molecular weight and CCS coded information from the dual TIMS funnel, dia PASEF enables most confident compound identification. Over the entire LC MS/MS dia PASEF runs a perfect data cuboid is created containing m/z, ion mobility (CCS) retention time and intensity. Here, to evaluate these benefits of dia PASEF, we compared gradient lengths and results from two independent software platforms which can process native dia PASEF data using spectral libraries or a library free approach.Summary: Here, to evaluate these benefits of dia PASEF, we compared gradient lengths and results from two independent software platforms which can process native dia PASEF data using spectral libraries or a library free approach.
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