AUDENS: a tool for automated peptide de novo sequencing.
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/ .
Grossmann
Jonas
J
Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zentrum, CH-8092 Zürich, Switzerland.
Roos
Franz F
FF
Cieliebak
Mark
M
Lipták
Zsuzsanna
Z
Mathis
Lucas K
LK
Müller
Matthias
M
Gruissem
Wilhelm
W
Baginsky
Sacha
S
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
D007477:Ions; D010455:Peptides; D010940:Plant Proteins; D003165:Complement System Proteins