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AUDENS: a tool for automated peptide de novo sequencing


Grossmann, J; Roos, F F; Cieliebak, M; Lipták, Z; Mathis, L K; Müller, M; Gruissem, W; Baginsky, S (2005). AUDENS: a tool for automated peptide de novo sequencing. Journal of Proteome Research, 4(5):1768-1774.

Abstract

We present AUDENS, a new platform-independent open source tool for automated de novo sequencing of peptides from MS/MS data. We implemented a dynamic programming algorithm and combined it with a flexible preprocessing module which is designed to distinguish between signal and other peaks. By applying a user-defined set of heuristics, AUDENS screens through the spectrum and assigns high relevance values to putative signal peaks. The algorithm constructs a sequence path through the MS/MS spectrum using the peak relevances to score each suggested sequence path, i.e., the corresponding amino acid sequence. At present, we consider AUDENS a prototype that unfolds its biggest potential if used in parallel with other de novo sequencing tools. AUDENS is available open source and can be downloaded with further documentation at http://www.ti.inf.ethz.ch/pw/software/audens/ .

Abstract

We present AUDENS, a new platform-independent open source tool for automated de novo sequencing of peptides from MS/MS data. We implemented a dynamic programming algorithm and combined it with a flexible preprocessing module which is designed to distinguish between signal and other peaks. By applying a user-defined set of heuristics, AUDENS screens through the spectrum and assigns high relevance values to putative signal peaks. The algorithm constructs a sequence path through the MS/MS spectrum using the peak relevances to score each suggested sequence path, i.e., the corresponding amino acid sequence. At present, we consider AUDENS a prototype that unfolds its biggest potential if used in parallel with other de novo sequencing tools. AUDENS is available open source and can be downloaded with further documentation at http://www.ti.inf.ethz.ch/pw/software/audens/ .

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
08 University Research Priority Programs > Systems Biology / Functional Genomics
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Language:English
Date:9 August 2005
Deposited On:18 Dec 2009 06:09
Last Modified:05 Apr 2016 13:35
Publisher:American Chemical Society
ISSN:1535-3893
Publisher DOI:https://doi.org/10.1021/pr050070a
PubMed ID:16212431

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