DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy

peer-reviewed · Nucleic Acids Research · 2005

peer-reviewed · Nucleic Acids Research · 2005. Brian D. Halligan et al. One of the core activities of high-throughput proteomics is the identification of peptides from mass spectra…

Date	2005-07-01
Type	peer-reviewed
Venue	Nucleic Acids Research
Publisher	Oxford University Press (OUP)
Contribution	adjacent
DOI	10.1093/nar/gki461
Citations (OpenAlex)	21
Venue 2-year citedness	16.42

Abstract

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 http://proteomics.mcw.edu/denovoid.

Authors

Methods and tools

DeNovoID: Web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing.

Cites (15)

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