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Bioinformatics Vol. 19 no. 6 2003
Pages 792-793
© 2003 Oxford University Press

Applications Note

Interpreting peptide mass spectra by VEMS

R. Matthiesen *, M. Lundsgaard , K.G. Welinder and G. Bauw

Department of Biotechnology, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark

Received on October 7, 2002 ; revised on November 20, 2002

Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution of masses up to 5000 Da. VEMSmaldi searches singly charged peptide masses against the local database.

Availability: http://www.bio.auc.dk/~rm/sub/VEMS.htm

Contact: rm{at}bio.auc.dk

* To whom correspondence should be addressed.


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