PNovo 3: precise de novo peptide sequencing using a learning-to-rank framework.

ABSTRACT:

Motivation

De novo peptide sequencing based on tandem mass spectrometry data is the key technology of shotgun proteomics for identifying peptides without any database and assembling unknown proteins. However, owing to the low ion coverage in tandem mass spectra, the order of certain consecutive amino acids cannot be determined if all of their supporting fragment ions are missing, which results in the low precision of de novo sequencing.

Results

In order to solve this problem, we developed pNovo 3, which used a learning-to-rank framework to distinguish similar peptide candidates for each spectrum. Three metrics for measuring the similarity between each experimental spectrum and its corresponding theoretical spectrum were used as important features, in which the theoretical sp

SUBMITTER: Yang H 

PROVIDER: S-EPMC6612832 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature