title: AUDENS: a tool for automated peptide de novo sequencing.
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/ .
authors.affiliation: Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zentrum, CH-8092 Zürich, Switzerland.
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.forename: Franz F
authors.initials: FF
authors.lastname: Roos
authors.forename: Mark
authors.initials: M
authors.lastname: Cieliebak
authors.forename: Zsuzsanna
authors.initials: Z
authors.lastname: Lipták
authors.forename: Lucas K
authors.initials: LK
authors.lastname: Mathis
authors.forename: Matthias
authors.initials: M
authors.lastname: Müller
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
authors.forename: Sacha
authors.initials: S
authors.lastname: Baginsky
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism; D003165:Complement System Proteins; D020407:Internet; D007477:Ions; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein / Q000295:instrumentation* / Q000379:methods*; D012984:Software
chemical_list: D007477:Ions; D010455:Peptides; D010940:Plant Proteins; D003165:Complement System Proteins