MSNovo: a dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry.

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...

A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (Extended Abstract)

De Novo Peptide Identification Via Mixed-Integer Linear Optimization And Tandem Mass Spectrometry

A novel methodology for the de novo identification of peptides via mixedinteger linear optimization (MILP) and tandem mass spectrometry is presented. The overall mathematical model is presented and the key concepts of the proposed approach are described. A pre-processing algorithm is utilized to identify important m/z values in the tandem mass spectrum. Missing peaks, due to residue-dependent f...

A Two-way Parallel Searching for Peptide Identification via Tandem Mass Spectrometry

De novo peptide sequencing that determines the amino acid sequence of a peptide via tandem mass spectrometry (MS/MS) has been increasingly used nowadays in proteomics for protein identification. Current de novo methods generally employ a graph theory, which usually produces a large number of candidate sequences and causes heavy computational cost while trying to determine a sequence with less a...

PepNovo: de novo peptide sequencing via probabilistic network modeling.

We present a novel scoring method for de novo interpretation of peptides from tandem mass spectrometry data. Our scoring method uses a probabilistic network whose structure reflects the chemical and physical rules that govern the peptide fragmentation. We use a likelihood ratio hypothesis test to determine whether the peaks observed in the mass spectrum are more likely to have been produced und...