Welcome to pep2pro - from peptide to proteome



pep2pro is a further development of AtProteome [link] and provides proteome information on Arabidopsis thaliana. The underlying proteome analysis database allowed integrating and analysing the large proteome datasets listed below (described in Hirsch-Hoffmann et al., 2012 [Link] and Baerenfaller et al., 2011 [Link]) and the website shows all the information about the protein identifications with a proteogenomic mapping of the peptides onto the genome. The pep2pro TAIR9 wos dataset is provided as the default dataset. The other datasets can be selected from the drop-down menu 'Choose the Assembly' and depending on the information available, the corresponding submenus will appear. The datasets marked with an asterisk are included in the MASCP Gator (http://gator.masc-proteomics.org).

For finding a protein in a dataset, click on 'Protein Search' and enter the search arguments. These can either be an ATG number (first 9 characters without the splice information, e.g. AT2G39730), or a word from the annotation line (e.g. activase). One can also enter several ATG numbers or several search terms in parallel, separated with space, comma, or semicolon). In order to retrieve more information about the identification, click on the protein of interest.

Please see the [help file] to get more information and to get an introduction to the other features of the website.

*) The datasets marked with an asterisk are included in the MASCP Gator (http://gator.masc-proteomics.org).
Dataset Spectra specFDR Distinct
peptides
Loci
Cassava 4.1 V6 database 34'151
Large-Scale Proteomics of the Cassava Storage Root
Hervé Vanderschuren, Evans Nyaboga, Jacquelyne S. Poon, Katja Baerenfaller, Jonas Grossmann, Matthias Hirsch-Hoffmann, Norbert Kirchgessner,Paolo Nanni and Wilhelm Gruissem
Large-Scale Proteomics of the Cassava Storage Root and Identification of a Target Gene to Reduce Postharvest Deterioration
The Plant Cell 2014 [Link]
26'286 <1% 10'079 2'632
TAIR10 database 27'416
Agron-omics Long Day Optimal Watering (LOW) experiment *)
Baerenfaller K, Massonnet C, Hennig L, Russenberger D, Sulpice R, Walsh S, Stitt M, Granier C and Gruissem W
A long photoperiod relaxes energy management in Arabidopsis leaf six
Current Plant Biology 2015 [Link]
2applies to spectra containing quantitative information
50'947 2 0.07% 2 6'178 2 1'788 2
Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues *)
Tissue-specific total protein extracts 104'951 0.6% 6'887 1'799
Tissue-specific ubiquitin affinity enrichments
Svozil S., Gruissem W. and Baerenfaller K.
Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues
Frontiers 2015 [Link]
33'111 1.6% 3'901 1'123
Response to inhibition of the proteasome with Syringolin A *)
EDEN wt leaf full extract 543'626 0.3% 23'746 4'043
EDEN wbR48 transgenic line leaf full extract 247'355 0.3% 18'073 3'615
Ubiquitin affinity enrichment leaf 84'914 0.9% 10'559 2'242
Ubiquitin affinity enrichment root 87'846 0.6% 16'069 3'430
Tandem affinity enrichment
Svozil S., Hirsch-Hoffmann M., Dudler R., Gruissem W. and Baerenfaller K.
Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with Syringolin A
MCP 2014 [Link]
27'958 1.0% 3'159 905
Protein accumulation in APG mutants *)
Motohashi R, Rödiger A, Agne B, Baerenfaller K and Baginsky S
Common and specific protein accumulation patterns in different albino/pale green (apg) mutants reveals regulon organization at the proteome level
Plant Physiology 2012 [Link]
205'369 0.4% 15'240 3'437
Agron-omics Short Day Optimal Watering (SOW) experiment *) 144'538 2 0.09% 2 8'710 2 2'081 2
Agron-omics Short Day Mild Water Deficit (SWD) experiment *)
Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C and Gruissem W
Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit
Molecular Systems Biology 2012 [Link]
2applies to spectra containing quantitative information
74'550 2 0.1% 2 5'292 2 1'509 2
pep2pro TAIR10 wos *) (without single hits) 2'669'654 0.7% 141'934 14'582
TAIR9 database 27'379
Plastid Proteome Assembly in absence of Toc159 *)
Sylvain Bischof, Katja Baerenfaller, ThomasWildhaber, Raphael Troesch, Pierre-Alexandre Vidi, Bernd Roschitzki, Matthias Hirsch-Hoffmann, Lars Hennig, Felix Kessler, Wilhelm Gruissem and Sacha Baginsky
Plastid Proteome Assembly without Toc159: Photosynthetic Protein Import and Accumulation of N-Acetylated Plastid Precursor Proteins.
The Plant Cell November 2011 [Link]
296'571 0.52% 29'524 5'159
Comparative phosphoproteome study of the STN8 kinase mutant *)
Reiland S., Finazzi G., Endler A., Willig A., Baerenfaller K., Grossmann J., Gerrits B., Rutishauser D., Gruissem W., Rochaix J-D. and Baginsky S.
Comparative phosphoproteome profiling reveals a function of theSTN8 kinase in fine-tuning of cyclic electron flow (CEF).
PNAS 2011 [Link]
1applies to phosphoproteome data
15'492 1 0.15% 1 3'589 1 1'738 1
AtProteome TAIR9 803'530 1.0% 87'630 13'290
AtProteome TAIR9 extended 1'066'363 1.0% 97'010 14'378
pep2pro TAIR9 2'664'441 0.9% 144'824 18'111
pep2pro TAIR9 wos (without single hits)
Katja Baerenfaller, Matthias Hirsch-Hoffmann, Julia Svozil, Roger Hull, Doris Russenberger, Sylvain Bischof, Qingtao Lu, Wilhelm Gruissem and Sacha Baginsky
pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana
Integr. Biol., 2011, 3, 225-237 [Link]
2'660'852 0.7% 141'235 14'522
TAIR8 database 27'235
Arabidopsis thaliana leaf wound proteome *)
Gfeller A., Baerenfaller K., Loscos J., Chételat A., Baginsky S. and Farmer E.
Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves.
Plant Physiology 2011 [Link]
216'896 1.0% 29'908 6'530
AtProteome TAIR8 799'292 1.0% 86'763 13'104
AtProteome TAIR8 extended 1'062'435 1.0% 96'145 14'195
Large-scale phosphoproteome analysis of Arabidopsis thaliana shoots
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., and Baginsky S.
Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
Plant Physiology 2009 [Link]
4'905
TAIR7 database 27'029
AtProteome TAIR7 (original)
Baerenfaller K., Grossmann J., Grobei M.A., Hull R., Hirsch-Hoffmann M., Yalovsky S., Zimmermann P., Grossniklaus U., Gruissem W. and Baginsky S.
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.
Science 2008 [Link]
790'181 0.9% 86'456 13'029
AtProteome TAIR7 803'577 1.0% 86'966 13'154
Pollen proteome map of Arabidopsis thaliana TAIR7
Grobei MA et al.
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
Genome Research, 2009
4'436


News

28 July 2015, Public release of the Agron-omics long day optimal water (LOW) dataset after publication of the article 'A long photoperiod relaxes energy management in Arabidopsis leaf six' in Current Plant Biology

11 May 2015, Public release of the datasets 'Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues' after publication of the article in Frontiers in Plant Science

30 May 2014, Public release of the dataset 'Proteome characterization of the cassava root' after publication of the article in The Plant Cell

13 April 2014, Public release of the datasets 'Response to inhibition of the proteasome with Syringolin A' after publication of the article in Molecular & Cellular Proteomics

01 October 2012, Public release of the dataset 'Protein accumulation in APG mutants' upon publication in Plant Physiology

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