PepNovo statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PepNovo
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Tool usage distribution map

This map represents all the scientific publications referring to PepNovo per scientific context
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Associated diseases

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Protocols

PepNovo specifications

Information


Unique identifier OMICS_02474
Name PepNovo
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Ari Frank

Information


Unique identifier OMICS_02474
Name PepNovo
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

Maintainer


This tool is not maintained anymore.

Publications for PepNovo

PepNovo citations

 (36)
library_books

Elucidation of cross species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

2018
BMC Evol Biol
PMCID: 5819086
PMID: 29463217
DOI: 10.1186/s12862-018-1141-1

[…] se of a dedicated algorithm (for example MASCOT, Byonic or MaxQuant; [–]), or through de novo only protein sequencing without a provided protein sequence database (for example PEAKS de novo, NOVOR or PepNovo; [–]). De novo algorithms suffer from high rates of incorrect peptide sequence identifications, however []. Hence, the adoption of error-tolerant algorithms that utilize protein sequence datab […]

library_books

Software aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry

2017
PLoS One
PMCID: 5665424
PMID: 29091918
DOI: 10.1371/journal.pone.0186461

[…] ere developed for full scan/data-dependent MS/MS peptide data interpretation. These approaches include four main groups: database searching (SEQUEST, MASCOT, etc.), de novo peptide sequencing (PEAKS, PepNovo, etc.), peptide sequence tagging (GutenTag) and consensus of multiple search engines (Scaffold) []. These MS-based proteomics approaches have difficulties with sequencing cyclic peptides witho […]

library_books

Data from proteome analysis of Lasiodiplodia theobromae (Botryosphaeriaceae)

2017
PMCID: 5447515
PMID: 28580409
DOI: 10.1016/j.dib.2017.04.058

[…] d explore peptides via sequence homology with sequenced proteins found in the entire Uniprot database using BLAST. The program DeNovoGUI version 1.14.5 was used for this purpose , and both Novor and PepNovo were used for peptide sequencing. The mass allowance parameters were, for precursor mass tolerance: 10 ppm, and a fragment mass tolerance of 0.5 Da. Post-translational modification settings c […]

library_books

A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses

2017
PMCID: 5464308
PMID: 28603547
DOI: 10.1186/s13015-017-0104-1

[…] several minutes for one spectrum). We refer to Additional file : Figure S8 for a more detailed comparison of the running times. We note that the running times of state-of-the-art software packages as PepNovo [], PEAKS [], and especially Novor [] are by magnitudes faster than the running times of our algorithm. However, we do not aim for an advanced software toolkit for de novo sequencing in this s […]

call_split

Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae)

2017
PMCID: 5802045
PMID: 29450146
DOI: 10.1016/j.biopen.2017.03.001
call_split See protocol

[…] explore peptides via sequence homology with sequenced proteins found in the entire Uniprot database using BLASTp. The program DeNovoGUI version 1.14.5 was used for this purpose , and both Novor and PepNovo were used for peptide sequencing. The mass allowance parameters were, for precursor mass tolerance: 10 ppm, and a fragment mass tolerance of 0.5 Da. Post-translational modification settings c […]

call_split

Dereplication of peptidic natural products through database search of mass spectra

2016
Nat Chem Biol
PMCID: 5409158
PMID: 27820803
DOI: 10.1038/nchembio.2219
call_split See protocol

[…] y compares a spectrum against all peptides with similar mass, the number of peptides to compare against is much smaller than the PNP database size. We score a PSM formed by Peptide and Spectrum using PepNovo and MS-GF+.SPCscore(Peptide, Spectrum) is defined as the Shared Peak Count, the number of peaks shared between Spectrum(Peptide) and the filtered version of Spectrum as defined by PepNovo., T […]


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PepNovo institution(s)
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
PepNovo funding source(s)
Supported by the “National Center for Research Resources” of the NIH via grant P-41-RR24851.

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