PepNovo statistics

info info

Citations per year

info

Popular tool citations

chevron_left De novo peptide sequencing chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

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

Download


download.png
docker.png
conda.png

Versioning


No version available

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

 (28)
library_books

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

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

[…] 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 […]

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

[…] 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 […]

library_books

Data from proteome analysis of Lasiodiplodia theobromae (Botryosphaeriaceae)

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

[…] 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 […]

library_books

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

[…] 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 […]

library_books

Multi species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks*

2016
PMCID: 5098046
PMID: 27609420
DOI: 10.1074/mcp.O116.060913

[…] p values of spectral pairs matched to the spectrum based on the score histogram. each ms/ms spectrum was converted into a prefix-residue mass (prm) spectrum (scored version of spectrum) using pepnovo (), where ms/ms peak intensities were converted into log-likelihood scores by considering complementary ions (b/y), multiply charged ions, neutral losses (-h2o and -nh3), and 13c isotopes […]

library_books

Peptide de novo sequencing of mixture tandem mass spectra

2016
PMCID: 5297990
PMID: 27329701
DOI: 10.1002/pmic.201500549

[…] restriction by accurate mass measurements , , divide‐and‐conquer , or linear sequencing algorithms , are other methods used. some well‐known programs are sherenga , lutefisk , novohmm , peaks , pepnovo , and pnovo ., de novo sequencing approaches have recently received more attention due to the growing availability of high mass accuracy instrumentation . the best de novo algorithms […]


Want to access the full list of citations?
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.

PepNovo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PepNovo