] and provides proteome
information on Arabidopsis thaliana.
The underlying
proteome analysis database allowed integrating and analysing the large proteome
datasets listed below (described in Baerenfaller et al., 2011 [
]) 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 (
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.
] to get more information and to get an introduction
to the other features of the website.
| Dataset |
Spectra |
specFDR |
Distinct
peptides |
Loci |
| TAIR10 database |
27'416 |
| 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 |