A system and method to search spectral databases and to identify unknown materials from multiple spectroscopic data in the databases. The methodology may be substantially automated and is configurable to determine weights to be accorded to spectroscopic data from different spectroscopic data generating instruments for improved identification of unknown materials. Library spectra from known materials are divided into training and validation sets. Initial, instrument-specific weighting factors are determined using a weight grid or weight scale. The training and validation spectra are weighted with the weighting factors and indicator probabilities for various sets of “coarse” weighting factors are determined through an iterative process. The finally-selected set of coarse weighting factors is further “fine tuned” using a weight grid with finer values of weights. The instrument-specific finer weight values may be applied to test data sets (or spectra) of an unknown material as well as to the library spectra from corresponding spectroscopic instruments. Instrument-specific weights for each class of samples may also be computed for additional customization and accuracy.