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pNovo specifications


Unique identifier OMICS_02470
Name pNovo
Alternative name pNovo+
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes




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  • person_outline Hao Chi
  • person_outline Si-Min He

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Publications for pNovo

pNovo citations


SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics

Sci Rep
PMCID: 5294601
PMID: 28167817
DOI: 10.1038/srep41929
call_split See protocol

[…] The remaining unassigned spectra were pair-wisely (HCD-ETD) submitted to pNovo + (v.1.3). Precursor mass range was limited to between 700 to 4000 Da, oxidized methionine was considered as an independent residue, and mass tolerance was set at 5 ppm for precursors and 15 ppm […]


Human IgM Antibodies to Malondialdehyde Conjugated With Albumin Are Negatively Associated With Cardiovascular Disease Among 60‐Year‐Olds

PMCID: 5210446
PMID: 27998914
DOI: 10.1161/JAHA.116.004415
call_split See protocol

[…] lutamine as well as acetylation of protein N‐terminus as variable modifications. Peptide sequences with a <1% false discovery rate were excluded. The remaining data underwent de novo sequencing using pNovo+ (v.1.3) via a limited precursor mass range of 700 to 4000 Da, oxidized methionine as an independent residue, and mass tolerance set at 5 ppm for precursors and 15 ppm for fragments. Up to 9 top […]


Peptide de novo sequencing of mixture tandem mass spectra

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

[…] xture spectra deconvolution produced constantly high accuracy independent of mixture rate. The number of true identifications followed the trend similar to PEAKS (Fig. B) for all programs, except for pNovo+. The latter delivered more identifications from unprocessed data compared to deconvoluted one for mixture rates lower than 0.25. This type of performance could probably be explained by the char […]


Screening Method for the Discovery of Potential Bioactive Cysteine Containing Peptides Using 3D Mass Mapping

J Am Soc Mass Spectrom
PMCID: 4654750
PMID: 26552389
DOI: 10.1007/s13361-015-1282-z

[…] on spectra can be ‘manually’ interpreted or analyzed using specialized algorithms for automated de novo sequencing such as PEAKS (Bioinformatics Solutions Inc., Waterloo, ON, Canada), PepNovo [], and pNovo+ []. Full structure elucidation is only possible when complete fragmentation occurs and the spectrum is of sufficient quality with respect to signal-to-noise ratio. Instrumental parameters often […]


Mass Spectrometry Based Methods for Identifying Oxidized Proteins in Disease: Advances and Challenges

PMCID: 4496678
PMID: 25874603
DOI: 10.3390/biom5020378

[…] with iTRAQ-labeling quantification experiments and has been reported to remove approximately 10% of false positives []. Other software packages that aid in manual validation include PepNovo+, PEAKS, pNovo, MS-GFDB. UniNovo is reported to be best for manual validation of Orbitrap MS data []. Open source software to improve the user interface of packages such as PepNovo+ is also available []. A new […]


Identification of b /y ions in MS/MS spectra using a two stage neural network

Proteome Sci
PMCID: 3907776
PMID: 24565419
DOI: 10.1186/1477-5956-11-S1-S4

[…] window for peak selection. It selects the 6 most intense peaks in each 100 Da window []. In contrast, PILOT treats the whole spectrum as a single window and selects the top 125 most intense peaks []. pNovo similarly treats the entire sepctrum as a single window and selects the 100 most intense peaks []. This work improves upon our previous ion classifier []. In particular, we improved our modeling […]

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pNovo institution(s)
Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
pNovo funding source(s)
Supported by the National Key Research and Development Program of China (2016YFA0501301), the National High Technology Research and Development Program of China (863) under Grant 2014AA020902 and 2014AA020901, the National Natural Science Foundation of China (31470805) and Youth Innovation Promotion Association CAS (2014091).

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