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pep2pro specifications


Unique identifier OMICS_23296
Name pep2pro
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae


  • person_outline Katja Baerenfaller

Publication for pep2pro

pep2pro citations


Recreating the synthesis of starch granules in yeast

PMCID: 5119888
PMID: 27871361
DOI: 10.7554/eLife.15552.024

[…] were cloned by PCR. In the case of BE2, a shorter sequence than predicted was removed (48 instead of 61 amino acids) since a peptide starting from amino acid 49 has been detected in leaf proteomics (pep2pro database []). In addition to the ATG start codon, a glycine or alanine codon was introduced immediately downstream to improve the Kozak sequence (), if necessary (). A sequence codon-optimized […]


Exploring the potential of public proteomics data

PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] e specific databases have also been established, related to: diseases, for example TBDB for tuberculosis ; organisms, for example ProteomicsDB and the Human Proteome Map for the human proteome, and pep2pro for Arabidopsis ; or subproteomes, for example CSF‐PR for cerebrospinal fluid or TOPPR and TopFIND for in vivo cleaved proteins. For a comprehensive overview of the current proteomics datab […]


Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues

Front Plant Sci
PMCID: 4446536
PMID: 26074939
DOI: 10.3389/fpls.2015.00376

[…] yses. This does not apply to different splice variants of the same protein or to different loci sharing exactly the same amino acid sequence. All remaining spectrum assignments were inserted into the pep2pro database (Baerenfaller et al., ; Hirsch-Hoffmann et al., ). The false discovery rate (FDR) was calculated by dividing the number of reverse hits by the number of true hits times 100%. It was 0 […]


A New Parameterized Algorithm for Rapid Peptide Sequencing

PLoS One
PMCID: 3925086
PMID: 24551059
DOI: 10.1371/journal.pone.0087476

[…] To evaluate the sequencing accuracy and computational efficiency of the program on real experimental spectra, we obtained 10000 tandem mass spectra from the pep2pro organ-specific proteome map of Arabidopsis thaliana in the Proteomics Identification Database (PRIDE) . A preprocessing step is used to process the mass peaks in a spectrum before the sequenci […]


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pep2pro institution(s)
Department of Biology, ETH Zurich, Zurich, Switzerland; Faculty of Life Sciences, University of Manchester, Manchester, UK; Institute of Botany, Chinese Academy of Sciences, Beijing, China
pep2pro funding source(s)
Supported by the SystemsX initiative in the framework of the C-MOP project, and by the European Framework Programme 6 AGRON-OMICS project (LSHG-CT-2006-037704) and by the Chinese State Scholarship Program (grant number [2006]3036#).

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