Abstract: A method for performing library-free search analysis including performing a search using a spectrum-centric approach for a data; performing at least one of improving peptide centric analysis of a predicted spectral library by using the results of the spectrum centric search for creating a sub-selection of precursors, including a calibration by using results from the spectrum-centric approach; creating an optimized predicted library by refining static prediction models; using the calibration and/or the optimized predicted library to initiate a peptide-centric search for the data based on an in-silico library; creating a curated library by combining the results of the spectrum-centric approach with the results from the peptide-centric approach; and analyzing the results of the curated library using a second peptide-centric search of the data.

Abstract: Method for precursor identification from mass spectroscopic data as a function of mass to charge ratio, retention time as well as of ion mobility, using a database of reference precursor data for retrieval of a region of interest for at least three reference peptide precursors in the mass to charge ratio, the retention time as well as in the ion mobility dimension. In a first step for at least three reference precursors, from the database, said data is analysed in the precursor region of interest of mass to charge ratio, retention time as well as ion mobility dimension, and from that analysis empirically an adjusted center in the ion mobility dimension is determined and an ion mobility extraction width window is determined, and in a second step for the identification of further peptide precursors, said extraction width window is used.