Supplemental data
7. Ytterberg A.J., Peltier, J.B., van Wijk, K.J. (2006) Protein profiling
of plastoglobules in chloroplasts and chromoplasts; a surprising site for differential accumulation of
metabolic enzymes. Plant Physiology
- Supplemental Table 1. Peptide mass finger printing of chloroplast PG proteins separated by 1-DE gels.
- Supplemental Table 2. Comparative accumulation of the chloroplast PG proteome of stressed (D, HL) and unstressed leaves (C) based on differential stable isotope labeling.
6. Peltier, J.B., Cai, Y., Sun, Q., Zabrouskov, V., Giacomelli, L., Rudella,
A., Ytterberg, AJ, Rutschow, H., van Wijk, K.J. (2006) The oligomeric stromal proteome of A. thaliana
chloroplasts. Mol. Cell Proteomics
- Supplemental Table. All 241 proteins identified on the CN-PAGE of the chloroplast stroma proteome of Arabidopsis thaliana rosette leaves.
5. Majeran, W., Cai, Y., Sun, Q., van Wijk, K.J. (2005) Functional
differentiation of Bundle Sheath and Mesophyll maize chloroplasts determined by Comparative proteomics.
Plant Cell
- Supplemental Table 1. Identification of maize proteins in purified Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from three different types of experiments involving 2-DE gels, cICAT and LC-MS analysis of unlabeled peptides.
- Supplemental Table 2. Summary of identifications and quantifications obtained from the analysis of 2DE-IPG-PAGE for each protein spot that passed the criteria for reproducibility and that was used for quantification.
- Supplemental Table 3. Summary of the non-gel based comparative proteome analysis of BS and M chloroplast stroma using cICAT and parallel LS-MS runs.
- Supplemental Table 4. Complete list of quantifications for all type of comparative proteomics technique applied in this study. The quantification results were sorted following their functional classification.
4. Peltier, J-B, Ytterberg, A.J., Sun, Q. and van Wijk,
K.J. (2004) New functions of the thylakoid membrane proteome of Arabidopsis
thaliana revealed by a simple, fast and versatile fractionation strategy. J.
Biol. Chemistry
- Supplemental Table 1. Accession numbers, annotations and MS identification details of all 242 proteins identified by TPP analysis. Accession numbers, lab annotation, maximum probability based Mowse scores, and Adapted MapMan Bin and simplified functional classifications are listed.
- Supplemental Table 2. All identified proteins in thylakoid and envelopes. These proteins were collectively identified in this and other experimental proteomics studies (9,25) (7,24,34). All thylakoid proteins (322+64) and envelope proteins (429) as used for the functional classification in Fig. 5B,C. Proteins were identified by large scale proteomics studies or in more 'classical' biochemical tools or forward or reverse genetics. The presence of a predicted cTP, curated TMD prediction by TMHMM, functional classification (BIN) and assignment into more general functional categories is listed for each accession. These proteins are grouped in 6 fractions, as follows: 1) only thylakoid (150), 2) only thylakoid and envelope (25), 3) thylakoid and envelope and total chloroplast (74), 4) only envelope (222), 5) only envelope and total chloroplast (108), 6) only thylakoid and total chloroplast (135).
3. Sun, Q., Emanuelsson, O., van Wijk, K.J. (2004) Analysis of curated
and predicted plastid subproteomes of Arabidopsis. Subcellular
compartmentalization leads to distinctive proteome properties. Plant
Physiology 15, 723-734
2. Friso*, G., Giacomelli*, L., Ytterberg*, A.J., Peltier*, J.B.,
Rudella, A. Sun, Q., van Wijk, K.J. (2004) In-depth analysis of the thylakoid
membrane proteome of Arabidopsis thaliana chloroplasts; new proteins, new
functions and a plastid proteome database. Plant Cell 478-499 - * contributed equally
1. JB Peltier, D.R. Ripoll, G. Friso, A. Rudella, Y. Cai, J. Ytterberg,
L. Giacomelli, J. Pillardy, K. J van Wijk (2003) Clp protease complexes from
photosynthetic and non-photosynthetic plastids and mitochondria of plants, their
predicted 3-D structures and functional implications. Journal of Biological Chemistry
