Improving de novo Sequencing Accuracy for Ion Trap data in PEAKS Software
نویسندگان
چکیده
منابع مشابه
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...
متن کاملComplexity and scoring function of MS/MS peptide de novo sequencing.
Tandem mass spectrometry (MS/MS) has become a standard way for identifying peptides and proteins. A scoring function plays an important role in the MS/MS data analysis. De novo sequencing is the computational step to derive a peptide sequence from an MS/MS spectrum, normally by constructing the peptide that maximizes the scoring function. A number of polynomial time algorithms have been develop...
متن کاملA Comparative Study of Peptide Sequencing Software Tools for MS/MS
Overview MS/MS spectra of known and unknown peptides were used to study the performance of several de novo sequencing and database search programs. Proteins of the unknown peptides are not in databases, thereby necessitating de novo sequencing for identification. Three de novo sequencing programs, PEAKS, BioAnalyst, and Lutefisk were compared in this study. PEAKS provided the most reliabl...
متن کاملpNovo: de novo peptide sequencing and identification using HCD spectra.
De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. However, de novo sequencing can correctly interpret only approximately 30% of high- and medium-quality spectra generated by collision-induced dissociation (CID), which is much less than database search. This is mainly due to incomplete fragmentation and overlap o...
متن کاملPEAKS 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...
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