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DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. Nucleic Acids Res 2005 Jul 01;33(Web Server issue):W376-81 PMID: 15980493 PMCID: PMC1160222


One of the core activities of high-throughput proteomics is the identification of peptides from mass spectra. Some peptides can be identified using spectral matching programs like Sequest or Mascot, but many spectra do not produce high quality database matches. De novo peptide sequencing is an approach to determine partial peptide sequences for some of the unidentified spectra. A drawback of de novo peptide sequencing is that it produces a series of ordered and disordered sequence tags and mass tags rather than a complete, non-degenerate peptide amino acid sequence. This incomplete data is difficult to use in conventional search programs such as BLAST or FASTA. DeNovoID is a program that has been specifically designed to use degenerate amino acid sequence and mass data derived from MS experiments to search a peptide database. Since the algorithm employed depends on the amino acid composition of the peptide and not its sequence, DeNovoID does not have to consider all possible sequences, but rather a smaller number of compositions consistent with a spectrum. DeNovoID also uses a geometric indexing scheme that reduces the number of calculations required to determine the best peptide match in the database. DeNovoID is available at

Author List

Halligan BD, Ruotti V, Twigger SN, Greene AS


Andrew S. Greene PhD Interim Vice Chair, Chief, Professor in the Biomedical Engineering department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Amino Acids
Databases, Protein
Mass Spectrometry
Sequence Analysis, Protein
User-Computer Interface

View this publication's entry at the Pubmed website PMID: 15980493
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