Details of the experimenal sources:
 

Source IDDescription
28Analysis of lumenal and peripheral thylakoid proteome from A. thaliana chloroplasts extracted with Na2CO3, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF) (Q-TOF). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
36Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is fromthe proteome soluble in C/M (1:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
39Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is fromthe proteome soluble in C/M (1:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
44Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion by acid hydrolysis, trypsin or chemotrypsin and nanoLC-ESI-MS/MS (Q-TOF). This sample is the acetone extracted proteome. Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
45Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is from the lower phase of extraction with C/M (9:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
46Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is from the upper phase of extraction with C/M (9:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
47Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is from proteins extracted and soluble in C/M (1:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
48Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is from the insoluble pellet of C/M (1:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
101Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using sequential extraction with Acetone/Chloroform/Methanol, followed by 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). This is from the upper phase of extraction with C/M (9:1). Alll data were published in Friso et al (2004) Plant Cell 16, 478-499
105Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using "Three Phase Partitioning - TPP", followed by 1-D SDS PAGE, in gel digestion with trypsin and nanoLC-ESI-MS/MS (Q-TOF). All data were published in Peltier et al. (2004) JBC 279 (47), 49367-49383. After publication, all MS data were reanalyzed against ATHv6 and new filter
106Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using "Three Phase Partitioning - TPP", followed by 1-D SDS PAGE, in gel digestion with trypsin and nanoLC-ESI-MS/MS (Q-TOF). All data were published in Peltier et al. (2004) JBC 279 (47), 49367-49383. After publication, all MS data were reanalyzed against ATHv6 and new filter
107Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using "Three Phase Partitioning - TPP", followed by 1-D SDS PAGE, in gel digestion with trypsin and nanoLC-ESI-MS/MS (Q-TOF). All data were published in Peltier et al. (2004) JBC 279 (47), 49367-49383. After publication, all MS data were reanalyzed against ATHv6 and new filter
115Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using "Three Phase Partitioning - TPP", followed by 1-D SDS PAGE, in gel digestion with trypsin and nanoLC-ESI-MS/MS (Q-TOF). All data were published in Peltier et al. (2004) JBC 279 (47), 49367-49383
122Analysis of stripped thylakoid membrane proteome from A. thaliana chloroplasts. The membrane proteome was fractionationated using "Three Phase Partitioning - TPP", followed byin solution digestion with trypsin and nanoLC-ESI-MS/MS (Q-TOF). All data were published in Peltier et al. (2004) JBC 279 (47), 49367-49383. After publication, all MS data were reanalyzed against ATHv6 and new filter
1332-DE gel analysis of Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. Purified M chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1362-DE gel analysis of Bundle sheath (BS) chloroplast stroma from maize (T43) leaf tips. Purified BS chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1372-DE gel analysis of Bundle sheath (BS) chloroplast stroma from maize (T43) leaf tips. Purified BS chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1432-DE gel analysis of Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. Purified M chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1442-DE gel analysis of Bundle sheath (BS) chloroplast stroma from maize (T43) leaf tips. Purified BS chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1452-DE gel analysis of Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. Purified M chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1462-DE gel analysis of Bundle sheath (BS) chloroplast stroma from maize (T43) leaf tips. Purified BS chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140.
1472-DE gel analysis of Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. Purified M chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1482-DE gel analysis of Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. Purified M chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
151Analysis of the native stromal proteome of A. thaliana chloroplasts. The stromal proteome was separated first by CN-PAGE, folllowed by SDS-PAGE. Proteins were identified by MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data are published in Peltier et al. (2006) Molec. Cell. Proteomics 5 (1), 514-533
155Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using (parallel) quantitication of extracted single ion chromatograms from nanoLC-ESI mass spectrometry of trypsin digested MS and B stromal proteomes. Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
156Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using (parallel) quantitication of extracted single ion chromatograms from nanoLC-ESI mass spectrometry of trypsin digested MS and B stromal proteomes. Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
157Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using (parallel) quantitication of extracted single ion chromatograms from nanoLC-ESI mass spectrometry of trypsin digested MS and B stromal proteomes. Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
158Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using (parallel) quantitication of extracted single ion chromatograms from nanoLC-ESI mass spectrometry of trypsin digested MS and B stromal proteomes. Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
168Analysis of lumenal and peripheral thylakoid proteome from 1 day high light (1000 uE/m2.s) treated wt A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
169Analysis of lumenal and peripheral thylakoid proteome from 1 day high light (1000 uE/m2.s) treated wt A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
170Analysis of lumenal and peripheral thylakoid proteome from A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
171Analysis of lumenal and peripheral thylakoid proteome from A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
172Analysis of lumenal and peripheral thylakoid proteome from A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
173Analysis of lumenal and peripheral thylakoid proteome from A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
180Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF). This is biological replicate #1
181Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent.. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).This is biological replicate #1
1822-DE gel analysis of Bundle sheath (BS) chloroplast stroma from maize (T43) leaf tips. Purified BS chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
1832-DE gel analysis of Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. Purified M chloroplast stromal proteome was separated by isoelectric focussing (IPG strips, pI4-7) and 1-D SDS PAGE, in gel digestion and MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF). Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
187Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent.After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).This is biological replicate #2
188Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent.. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).This is biological replicate #2
194Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana ffc1-1 (SRP54 KO) mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent.After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).
195Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana ffc1-1 (SRP54 KO) mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).
201Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using cICAT (cleavable stable isotope affinity tags), followed by identification and quantification by 2-D-LC-ESI mass spectrometry.Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
202Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using cICAT (cleavable stable isotope affinity tags), followed by identification and quantification by 2-D-LC-ESI mass spectrometry.Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
210Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using cICAT (cleavable stable isotope affinity tags), followed by 1-D gel separation and identification and quantification by nanoLC-ESI mass spectrometry.Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
211Comparative proteome analysis of Bundle sheath (BS) and Mesophyll (M) chloroplast stroma from maize (T43) leaf tips. BS/M expression ratio's were determined using cICAT (cleavable stable isotope affinity tags), followed by 1-D gel separation and identification and quantification by nanoLC-ESI mass spectrometry.Data were published in Majeran et al. (2005) Plant Cell 17, 3111-3140
217Analysis of lumenal and peripheral thylakoid proteome from A. thaliana chloroplasts extracted by sonication, followed by isoelectric focussing (IPG strips) and 1-D SDS PAGE, in gel digestion and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Giacomelli etal (2006) Plant Physiology 141(2) 685-701
218Plastoglobule proteome analysis from wt (Col-0) Arabidopsis thaliana chloroplasts. plastoglobules were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF). Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
219Plastoglobule proteome analysis from wt (Col-0) Arabidopsis thaliana chloroplasts. plastoglobules were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
220Plastoglobule proteome analysis from wt (Col-0) Arabidopsis thaliana chloroplasts. plastoglobules were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
221Plastoglobule proteome analysis from high-light treated wt (Col-0) Arabidopsis thaliana chloroplasts. Plants were grown under optimal conditions and then exposed to continuous 1000 uE.m2.sec for 7 days. plastoglobules were extracted from chloroplasts by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
222Plastoglobule proteome analysis from high-light treated wt (Col-0) Arabidopsis thaliana chloroplasts. Plants were grown under optimal conditions and then exposed to continuous 1000 uE.m2.sec for 7 days. plastoglobules were extracted from chloroplasts by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
223Plastoglobule proteome analysis from high-light treated wt (Col-0) Arabidopsis thaliana chloroplasts. Plants were grown under optimal conditions and then exposed to continuous 1000 uE.m2.sec for 7 days. plastoglobules were extracted from chloroplasts by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
224Plastoglobule proteome analysis from dark treated wt (Col-0) Arabidopsis thaliana chloroplasts. Plants were grown under optimal conditions and then kept for 7 days in complete darkness. Plastoglobules were extracted from chloroplasts by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
225Plastoglobule proteome analysis from dark treated wt (Col-0) Arabidopsis thaliana chloroplasts. Plants were grown under optimal conditions and then kept for 7 days in complete darkness. Plastoglobules were extracted from chloroplasts by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
226Plastoglobule proteome analysis from the Arabidopsis thaliana mutant clpr2-1. Chloroplast were purified and plastoglobules were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
228Low Density Lipid Body (LDLB) proteome analysis from rice etioplasts. Etioplasts were purified and LDLB (plastoglobules and prolamellar bodies) were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by in-solution trypsination and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
235Plastoglobule proteome analysis from the Arabidopsis thaliana wt Chloroplast were purified and plastoglobules were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by 1D SDS-PAGE and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
241Analysis of the oligomeric thylakoid proteome of maize (T43) mesophyll chloroplasts. The thylakoid membrane was solubilized by the detergent DM and then separated first by BN-PAGE, folllowed by SDS-PAGE. Proteins were identified by MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF)
248Analysis of the oligomeric thylakoid proteome of mixed maize Bundle Sheath & Mesophyll chloroplasts from "WT" for comparison to the hcf136 mutant. The thylakoid membrane was solubilized by the detergent DM and then separated first by BN-PAGE, folllowed by SDS-PAGE. Proteins were identified by MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing. Samples for MS analysis mixed with matching hcf136 samples.
249Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana ffc1-2 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).- Biological exp 2.
250Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana ffc1-2 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).- Biological exp 2.
251Analysis of the oligomeric thylakoid proteome of maize mesophyll and bundle sheath chloroplasts. The thylakoid membranes were solubilized by the detergent DM and then diluted 10-fold and then separated first by BN-PAGE, folllowed by SDS-PAGE. Proteins were identified by MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF) . Matched spots of BS and M thylakoids were mixed prior to MS analysis.
252Analysis of the oligomeric thylakoid proteome of maize mesophyll and bundle sheath chloroplasts. The thylakoid membranes were solubilized by the detergent DM and then diluted 10-fold and then separated first by BN-PAGE, folllowed by SDS-PAGE. Proteins were identified by MALDI-TOF MS (Voyager DE-STR) peptide mass finger printing and/or nanoLC-ESI-MS/MS (Q-TOF) . Matched spots of BS and M thylakoids were mixed prior to MS analysis.
264Plastoglobule proteome analysis from the Arabidopsis thaliana mutant clpr2-1. Chloroplast were purified and plastoglobules were extracted by sonication, followed by purification through sucrose gradient flotations. Proteins were identified by 1D SDS-PAGE and nanoLC-ESI-MS/MS (Q-TOF).Data are published in Ytterberg etal (2006) Plant Physiology140(3):984-97
272Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF). This is biological replicate #3
273Comparative chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant and wt (both col-0).Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and labeled by cICAT reagent. After mixing with wt cICAT labeled proteome, and SDS-PAGE separation, 12 bands were proteins were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF). This is biological replicate #3
274Shotgun analysis of the chloroplast stromal proteome analysis of the Arabidopsis thaliana wt plants (col-0) for label free comparison with clpr2-1. Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and.run out on SDS-PAGE . 12 bands were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF). This is technical replicate #1.
275Shotgun analysis of the chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant (col-0) for label free comparison with wt. Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and run out on SDS-PAGE . 12 bands were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF). This is technical replicate #1.
278Shotgun analysis of the chloroplast stromal proteome analysis of the Arabidopsis thaliana wt plants (col-0) for label free comparison with clpr2-1. Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and.run out on SDS-PAGE . 12 bands were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF).This is technical replicate #1 - bands 1-8 only. Same samples as experiment #274
279Shotgun analysis of the chloroplast stromal proteome analysis of the Arabidopsis thaliana clpr2-1 mutant (col-0) for label free comparison with wt. Intact chloroplasts were purified from fully grown leaf rosettes, and stroma was collected by ultracentrifugation of lysed chloroplasts and.run out on SDS-PAGE. 12 bands were trypsinized and quantified by nanoLC-ESI-MS and identified by nanoLCESI-MS/MS (Q-TOF). This is technical replicate #2-bands 1-8 only. Same samples as experiment #275
303Analysis of the chloroplast stromal proteome of the Arabidopsis thaliana wt plants (col-0). Stroma was purified from fully grown leaf rosettes, run out on SDS-PAGE . 12 bands were trypsinized overnight, peptides purified by C18 zip tips, and analyzed by RP-LC-ESI-LTQ-Orbitrap in triplicate (3x). This is biological replicate #1.
326Analysis of the chloroplast stromal proteome of the Arabidopsis thaliana wt plants (col-0). Stroma was purified from fully grown leaf rosettes, run out on SDS-PAGE . 12 bands were trypsinized overnight, peptides purified by C18 zip tips, and analyzed by RP-LC-ESI-LTQ-Orbitrap once (1x). This is biological replicate #2. - the corresponding thylakoid sample was analyzed under experiment #327.
327Analysis of the chloroplast thylakoid proteome of the Arabidopsis thaliana wt plants (col-0). Thylakoids were colected from isolated chloroplast of fully grown leaf rosettes, run out on SDS-PAGE . 12 bands were trypsinized overnight, peptides purified by C18 zip tips, and analyzed by RP-LC-ESI-LTQ-Orbitrap in duplo (2x). This from biological replicate #2 - the corresponding stromal sample was analyzed under experiment #326.
339Analysis of the chloroplast stroma proteome of the Arabidopsis thaliana wt plants (col-0). Stroma was purified from fully grown leaf rosettes, run out on SDS-PAGE . 12 bands were trypsinized overnight, peptides purified by C18 zip tips, and analyzed by RP-LC-ESI-LTQ-Orbitrap once (1x). This is from biological replicate #3 - the corresponing thylakoid sample was analyzed under experiment #343 and corresponding low density membrane fraction uder experiment #342.
342Analysis of the chloroplast low densitity proteome of the Arabidopsis thaliana wt plants (col-0). Low density membranes were collected from stromal sample from intact chloroplasts of fully grown leaf rosettes, run out on SDS-PAGE . 12 bands were trypsinized overnight, peptides purified by C18 zip tips, and analyzed by RP-LC-ESI-LTQ-Orbitrap in duplo (2x). This from biological replicate #3 - the stroma was analyzed under experiment #339 and correspoding thylakoids were analyzed under experiment #343.
343Analysis of the chloroplast thylakoid proteome of the Arabidopsis thaliana wt plants (col-0). Stroma was purified from fully grown leaf rosettes, run out on SDS-PAGE . 12 bands were trypsinized overnight, peptides purified by C18 zip tips, and analyzed by RP-LC-ESI-LTQ-Orbitrap in duplo (2x). This from biological replicate #3 - the corresponding stromal sample was analyzed under experiment #339.
359Comparative analysis of Bundle sheath and Mesophyll thylakoids by iTRAQ. The thylakoid membranes were delipidized and proteins "in-solution" digested with trypsin. BS and M derived peptides were differentially labeled with iTRAQ reagents and analyzed by nanoLC-ESI-MS/MS (Q-TOF) .
362Analysis of the oligomeric thylakoid proteome of maize (T43) mesophyll and bundle sheath chloroplasts. The thylakoid membranes were solubilized by the detergent DM and then separated first by BN-PAGE, folllowed by SDS-PAGE. Proteins were identified by nanoLC-ESI-MS/MS (Q-TOF).
393Comparative chloroplast thylakoid proteome analysis of the Arabidopsis thaliana ffc1-1 (SRP54 KO) mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and thylakoids were collected and stripped for peripheral proteins. Proteomes were digested and labeled with the iTRAQ reagent (four lables 114, 115, 116, 117), followed by SCX fractionation of the mixed labeled proteomes. Selected fractions were analyzed by nanoLCESI-MS/MS (Q-TOF). This is biological replicate 1. A more detailed description of the analysis can be found in Rutschow et al (submitted).
394Comparative chloroplast thylakoid proteome analysis of the Arabidopsis thaliana ffc1-1 (SRP54 KO) mutant and wt (both col-0). Intact chloroplasts were purified from fully grown leaf rosettes, and thylakoids were collected and stripped for peripheral proteins. Proteomes were digested and labeled with the iTRAQ reagent (four lables 114, 115, 116, 117), followed by SCX fractionation of the mixed labeled proteomes. Selected fractions were analyzed by nanoLCESI-MS/MS (Q-TOF). This is biological replicate 2. A more detailed description of the analysis can be found in Rutschow et al (submitted).
395Comparative total leaf proteome analysis of the Arabidopsis thaliana ffc1-1 (SRP54 KO) mutant and wt (both col-0). Total proteins were extracted from seedling in stage 1.07 (ffc and wt) as well as stage 1.11 (wt only). Proteomes were digested and labeled with the iTRAQ reagent (four lables 114, 115, 116, 117), followed by SCX fractionation of the mixed labeled proteomes. Selected fractions were analyzed by nanoLCESI-MS/MS (Q-TOF). This is biological replicate 1. A more detailed description of the analysis can be found in Rutschow et al (submitted).
396Comparative total leaf proteome analysis of the Arabidopsis thaliana ffc1-1 (SRP54 KO) mutant and wt (both col-0). Total proteins were extracted from seedling in stage 1.07 (ffc and wt) as well as stage 1.11 (wt only). Proteomes were digested and labeled with the iTRAQ reagent (four lables 114, 115, 116, 117), followed by SCX fractionation of the mixed labeled proteomes. Selected fractions were analyzed by nanoLCESI-MS/MS (Q-TOF). This is biological replicate 2. A more detailed description of the analysis can be found in Rutschow et al (submitted).
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