A spectrum library search is different from a sequence database search, which is commonly used in shotgun proteomics. The main difference is that in spectrum library searches, the measured spectra from your experiments are compared to libraries of measured (consensus) spectra from actual, previous experiments. Sequence database searches use theoretical spectra generated from peptide sequences.
Using a library of well-identified peptides avoids repeatedly identifying already known peptides via a time-consuming database search. Restricting the library to previously identified peptides also drastically reduces the search space and time. In addition, comparisons that use consensus spectra consider the measured peak intensities, which increases the selectivity and makes the identification more accurate.
The Proteome Discoverer application supports the following file formats:
- Standard MSP text format (.msp)
- SpectraST text format (.sptxt)
NOTE
You can import SpectraST format libraries, but the application does not support SpectraST searches.
- Archive containing a library file in a supported format, including NIST binary format. (.zip)
- Archive containing a library file in a supported format (.gz files (or .tar.gz))
The file must contain a complete spectrum library in MSPepSearch. If files are missing, the application does not add the library.
For information on changing the storage location of a spectral library, see Change the location of the spectral library files.