AUDENS: a tool for automated peptide de novo sequencing.

AuDeNS: A Tool for Automatic De Novo Peptide Sequencing

We have developed and implemented a framework for de novo sequencing of peptides using tandem mass spectrometry data. It first cleans the input spectrum with a number of data cleaning algorithms (“grass mowers”), followed by a sequencing algorithm that is a modification of a dynamic programming algorithm introduced in [CKT00]. In first experiments, our prototype performs well (but not better) i...

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

MOTIVATION The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem. RESULTS Very often, although the target...

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification*

Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. PEAKS DB achieves signi...

Appendix for UniNovo : a universal tool for de novo peptide sequencing

Open - pNovo : De Novo Peptide Sequencing with Thousands of 2 Protein

9 ABSTRACT: De novo peptide sequencing has improved remarkably, 10 but sequencing full-length peptides with unexpected modifications is 11 still a challenging problem. Here we present an open de novo 12 sequencing tool, Open-pNovo, for de novo sequencing of peptides 13 with arbitrary types of modifications. Although the search space 14 increases by ∼300 times, Open-pNovo is close to or even ∼10...