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J Proteome Res. 2008 Jul;7(7):3049-53. doi: 10.1021/pr800036d. Epub 2008 Jun 13.

Validation of endogenous peptide identifications using a database of tandem mass spectra.

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Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden.


The SwePep database is designed for endogenous peptides and mass spectrometry. It contains information about the peptides such as mass, pl, precursor protein and potential post-translational modifications. Here, we have improved and extended the SwePep database with tandem mass spectra, by adding a locally curated version of the global proteome machine database (GPMDB). In peptidomic experiment practice, many peptide sequences contain multiple tandem mass spectra with different quality. The new tandem mass spectra database in SwePep enables validation of low quality spectra using high quality tandem mass spectra. The validation is performed by comparing the fragmentation patterns of the two spectra using algorithms for calculating the correlation coefficient between the spectra. The present study is the first step in developing a tandem spectrum database for endogenous peptides that can be used for spectrum-to-spectrum identifications instead of peptide identifications using traditional protein sequence database searches.

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