Table 1 Proteins differentially accumulated and with functional assignment

 Abiotic Stress

Prupe.4G138700

0.997

1

Up_O1

Elongation factor 2

AT1G56070

Prupe.6G353600

0.154

0

Up_O1

Translational activator GCN1

AT1G64790

Prupe.3G043000

0.998

2

Up_O1

Developmentally-regulated G-protein 2

AT1G72660

Prupe.5G098100

0.643

1

Up_O1

Glutathione S-transferase T1

AT5G41210

 Actin Organization/Signaling

Prupe.6G320500

0.995

1

Up_O1

capping protein (actin filament) muscle Z-line, alpha (CAPZA)

AT3G05520

 Amino Acids Metabolism

Prupe.7G039100

0.366

0

Qualit_O1

Glutamate synthase (ferredoxin) / Ferredoxin-dependent glutamate synthase

AT5G04140

Prupe.5G056900

1

2

Qualit_O1

Glutamate dehydrogenase 2

AT5G07440

Prupe.5G171400

0.998

2

Up_O1

Anthranilate phosphoribosyltransferase / Phosphoribosyl-anthranilate pyrophosphorylase

AT5G17990

Prupe.6G249100

0.999

1

Up_O1

Diaminopimelate epimerase, chloroplastic

AT3G53580

Prupe.8G013600

1

2

Up_O1

ATP phosphoribosyltransferase / Phosphoribosyl-ATP pyrophosphorylase

AT1G09795

 Carbohydrate Metabolism/Abiotic Stress Response

Prupe.3G289900

1

2

Qualit_O1

GALACTINOL--SUCROSE GALACTOSYLTRANSFERASE 5-RELATED

AT5G40390

Prupe.7G248600

1

13

Qualit_O1

GALACTINOL--SUCROSE GALACTOSYLTRANSFERASE 6-RELATED

AT5G20250

Prupe.6G032400

0.115

0

Up_O1

Galactinol--sucrose galactosyltransferase / Raffinose synthase

AT1G55740

 Carbohydrates Metabolism

Prupe.3G192600

1

7

Qualit_O1

GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE SMALL SUBUNIT, CHLOROPLASTIC

AT5G48300

Prupe.6G076300

1

3

Qualit_O1

Triose-phosphate isomerase / Triosephosphate mutase

AT3G55440

Prupe.1G196700

1

5

Qualit_O1

Probable fructokinase-2

AT1G06030

Prupe.1G354000

1

2

Qualit_O1

1,4-alpha-glucan-branching enzyme 1, chloroplastic/amyloplastic

AT5G03650

Prupe.1G376200

1

6

Up_O1

GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE LARGE SUBUNIT 2, CHLOROPLASTIC

AT1G27680

Prupe.1G378500

0.998

2

Up_O1

SUGAR TRANSPORTER ERD6-LIKE 4-RELATED

AT1G75220

 Carbohydrates/Energy Metabolism

Prupe.4G124500

0.998

2

Qualit_O1

Isocitrate dehydrogenase [NADP]

AT1G54340

Prupe.3G288200

0.15

0

Up_O1

ISOCITRATE DEHYDROGENASE [NADP], CHLOROPLASTIC/MITOCHONDRIAL

AT5G14590

 Carbohydrates Metabolism/Redox Metabolism

Prupe.2G091600

0.5

1

Up_O1

Malate dehydrogenase (NADP(+)) / NADP-linked malate dehydrogenase

AT5G58330

 Carbohydrates Metabolism/Signaling

Prupe.4G110600

0.995

1

Up_O1

Phosphatase IMPL1, chloroplastic

AT1G31190

 Cell Division

Prupe.8G209400

0.283

0

Up_O1

CLIP-associated protein

AT2G20190

 Cell Wall Metabolism

Prupe.5G123800

0.998

2

Qualit_O1

CELLULOSE SYNTHASE-LIKE PROTEIN G1-RELATED

AT4G23990

Prupe.5G118000

0.999

2

Qualit_O1

ENDOGLUCANASE 19-RELATED

AT1G64390

 Cell Wall Metabolism/Signaling

Prupe.7G266700

0.122

0

Qualit_O1

Probable phosphoinositide phosphatase SAC9

AT3G59770

 Cellular Response to Light Intensity

Prupe.3G235100

0.998

2

Up_O1

Photosystem II repair protein PSB27-H1, chloroplastic

AT1G03600

 Cellular Response to Light Intensity/Abiotic Stress Response

Prupe.1G264900

0.998

2

Qualit_O1

Glutathione S-transferase

AT1G10370

 Chloroplast Photorelocation Movements

Prupe.1G498000

1

3

Up_O1

PLASTID MOVEMENT IMPAIRED1

AT1G42550

Prupe.1G263000

1

2

Up_O1

protein phosphatase 2A-2

AT1G10430

 Chloroplast protein import

Prupe.1G170300

1

3

Up_O1

Protein TIC 22-like, chloroplastic

AT3G23710

 Cofactor (Vit E) Metabolism

Prupe.1G023700

0.074

0

Up_O1

2-methyl-6-phytyl-1,4-hydroquinone methyltransferase, chloroplastic

AT3G63410

 Cytoskeleton Organization

Prupe.7G059400

0.479

0

Up_O1

Villin-2

AT2G41740

 Detoxification

Prupe.4G243800

0.998

2

Qualit_O1

ADP-ribose diphosphatase / ADPR-PPase // NAD(+) diphosphatase

AT4G25434

 Energy Metabolism

Prupe.2G325400

1

2

Qualit_O1

Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

AT3G03100

Prupe.1G231900

1

3

Up_O1

NADH dehydrogenase (ubiquinone) flavoprotein 1 (NDUFV1)

AT5G08530

Prupe.2G281900

0.998

2

Up_O1

ENOLASE

AT2G36530

Prupe.3G056600

1

10

Up_O1

6-PHOSPHOFRUCTOKINASE 1-RELATED

AT4G26270

 Esters Catabolism

Prupe.1G439300

0.998

2

Up_O1

CARBOXYLESTERASE 2-RELATED

AT1G47480

Prupe.8G121500

0.976

1

Up_O1

CARBOXYLESTERASE 12-RELATED

AT3G48700

 Hormones Metabolism/Signaling

Prupe.6G295900

0.217

0

Up_O1

RECEPTOR-LIKE PROTEIN KINASE FERONIA

AT3G51550

Prupe.6G065600

1

7

Up_O1

BR-signaling kinase (BSK)

AT5G59010

Prupe.8G250300

0.5

1

Up_O1

BRI1 suppressor 1 (BSU1)-like 1

AT4G03080

 Lactones Biosynthesis

Prupe.7G162300

0.998

2

Up_O1

3-hydroxyacyl-CoA dehydrogenase

AT3G51000

YES

 Lipids Metabolism

Prupe.4G132600

0.994

1

Qualit_O1

2,4-dienoyl-CoA reductase (NADPH) / 4-enoyl-CoA reductase (NADPH)

AT3G12800

Prupe.7G175400

0.989

0

Qualit_O1

PHOSPHOLIPASE D DELTA

AT4G35790

Prupe.8G162500

0.5

1

Up_O1

Phosphatidylinositol diacylglycerol-lyase / Phosphatidylinositol phospholipase C

AT4G38690

Prupe.3G064800

1

3

Qualit_O1

Peroxyureidoacrylate/ureidoacrylate amidohydrolase

AT3G16190

Prupe.6G180800

0.985

1

Up_O1

3-hydroxyacyl-[acyl-carrier-protein] dehydratase / D-3-hydroxyoctanoyl-[acyl carrier protein] dehydratase

AT5G10160

Prupe.5G079200

0.998

2

Qualit_O1

ACID CLUSTER PROTEIN 33

AT4G12230

YES

Prupe.1G512000

0.104

0

Up_O1

Acetyl-CoA carboxylase 1

AT1G36160

Prupe.3G176900

1

3

Qualit_O1

3-hydroxyisobutyryl-CoA hydrolase-like protein 5

AT1G06550

 Lipids/Redox Metabolism

Prupe.6G063600

1

5

Up_O1

neutral ceramidase (ASAH2)

AT1G07380

 Microtubules Organization

Prupe.6G088500

0.083

0

Qualit_O1

KINESIN MOTOR PROTEIN-RELATED PROTEIN-RELATED

AT3G45850

Prupe.1G083500

0.236

0

Up_O1

Protein MOR1

AT2G35630

Prupe.5G206800

0.998

2

Up_O1

PROTEIN SPIRAL1

AT1G26355

 Organelles Morphogenesis

Prupe.3G172600

1

2

Qualit_O1

peroxisomal and mitochondrial division factor 2

AT1G06530

Prupe.6G326600

1

4

Up_O1

Ras homolog gene family, member T1 (RHOT1, ARHT1)

AT5G27540

 Nucleosides and Nucleotides Biosynthesis

Prupe.3G304300

1

3

Up_O1

URIDINE KINASE

AT5G40870

 Peroxisome organization

Prupe.3G220500

0.5

1

Qualit_O1

Peroxisome biogenesis protein

AT3G21865

 Phenylpropanoids Metabolism

Prupe.2G319700

1

5

Qualit_O1

Caffeate O-methyltransferase

AT5G54160

Prupe.2G263900

1

4

Qualit_O1

CHALCONE--FLAVONONE ISOMERASE 3-RELATED

AT5G05270

Prupe.3G194000

1

2

Qualit_O1

Cinnamyl alcohol dehydrogenase

AT1G72680

 Photoperiodic Flowering Regulation

Prupe.6G149500

0.614

1

Qualit_O1

Ubiquitin carboxyl-terminal hydrolase 12

AT5G06600

 Polyamines metabolism

Prupe.5G078900

0.977

1

Qualit_O1

AMINE OXIDASE-RELATED

AT4G12290

Prupe.1G255300

0.5

1

Up_O1

spermidine synthase (speE, SRM)

AT1G23820

 Processing of Vacuolar Seed Protein Precursors

Prupe.5G076300

0.998

2

Up_O1

HEMOGLOBINASE FAMILY MEMBER

AT1G62710

 Protein Degradation

Prupe.8G251000

0.998

1

Qualit_O1

nuclear protein localization protein 4 homolog (NPLOC4, NPL4)

AT2G47970

 Protein Folding

Prupe.8G161100

1

9

Up_O1

PEPTIDYL-PROLYL CIS-TRANS ISOMERASE

AT2G16600

 Protein Modification

Prupe.2G212600

0.621

1

Up_O1

oligosaccharyltransferase complex subunit alpha (ribophorin I) (OST1, RPN1)

AT2G01720

 Protein Synthesis

Prupe.1G133900

1

6

Qualit_O1

Eukaryotic translation initiation factor 2 subunit 3

AT1G04170

Prupe.1G177100

0.999

2

Qualit_O1

Eukaryotic translation initiation factor 3 subunit H

AT1G10840

Prupe.3G187100

1

5

Up_O1

60S ribosomal protein L27-3

AT4G15000

Prupe.3G286600

0.998

2

Up_O1

Large subunit ribosomal protein L7/L12 (RP-L7, MRPL12, rplL)

AT3G27830

Prupe.7G052700

1

7

Up_O1

Eukaryotic translation initiation factor 3 subunit E

AT3G57290

 Protein Targeting

Prupe.3G089600

1

1

Up_O1

SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN

AT1G48900

 Pyrophosphate Metabolism and Photosynthate Partitioning

Prupe.3G091900

0.998

1

Qualit_O1

Inorganic pyrophosphatase (ppa)

AT1G15690

 Redox Metabolism

Prupe.2G051700

1

3

Qualit_O1

RING FINGER PROTEIN 41, 151

AT3G54360

 Regulation of L-ascorbic acid Biosynthetic Process

Prupe.5G179900

0.998

2

Qualit_O1

Mannose-1-phosphate guanyltransferase alpha

AT1G74910

 Regulation of Plant Cytokinesis/Abiotic Stress Response

Prupe.5G105500

0.997

1

Up_O1

MITOGEN-ACTIVATED PROTEIN KINASE 5

AT4G01370

 Regulation of Translation

Prupe.6G154800

0.054

0

Qualit_O1

Protein argonaute 4

AT2G27040

 RNA biogenesis

Prupe.2G121400

0.998

2

Up_O1

DNA-directed RNA polymerases II and IV subunit 5A

AT3G22320

 RNA biogenesis/Abiotic Stress Response

Prupe.1G346100

1

3

Qualit_O1

ATP-dependent RNA helicase (EIF4A3, FAL1)

AT3G19760

 RNA Splicing

Prupe.3G036300

0.135

0

Qualit_O1

116 kDa U5 small nuclear ribonucleoprotein component (EFTUD2)

AT1G06220

Prupe.2G275100

0.564

0

Up_O1

SPLICING FACTOR 1

AT5G51300

 Scaffolds in Cellular Signaling and Trafficking

Prupe.5G125200

0.772

1

Qualit_O1

KINESIN LIGHT CHAIN

AT4G10840

 Solute Transport

Prupe.1G460700

0.563

1

Qualit_O1

Plasma membrane ATPase 4

AT2G24520

 Specialized Metabolsim

Prupe.6G325100

1

4

Up_O1

Aryldialkylphosphatase / Phosphotriesterase

AT3G05350

YES

Prupe.3G026100

1

2

Up_O1

Cycloartenol synthase / 2,3-epoxysqualene--cycloartenol cyclase

AT2G07050

Prupe.4G002700

1

2

Up_O1

Farnesyl pyrophosphate synthase 2

AT5G47770

Prupe.2G160700

0.999

2

Up_O1

(+)-neomenthol dehydrogenase

AT3G61220

 Telomerase biogenesis

Prupe.6G137000

0.998

1

Up_O1

RuvB-like protein 1

AT5G22330

 Vacuolar Protein Sorting

Prupe.1G453100

0.5

1

Up_O1

AP-4 COMPLEX SUBUNIT BETA-1

AT5G11490

Prupe.2G056200

1

4

Up_O1

AP-4 complex subunit epsilon-1 (AP4E1)

AT1G31730

Prupe.1G365900

0.39

0

Up_O1

AP-2 complex subunit sigma-1 (AP2S1)

AT1G47830

 Vesicles Trafficking

Prupe.1G181200

0.285

0

Qualit_O1

Ras-related protein Rab-11A (RAB11A)

AT1G05810

Prupe.1G486400

0.27

0

Qualit_O1

TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 9

AT5G11040

Prupe.8G013500

0.998

2

Up_O1

Ras-related protein Rab-18 (RAB18) // protein phosphatase 1L [EC:3.1.3.16] (PPM1L, PP2CE)

AT1G43890

Prupe.3G293600

0.53

1

Up_O1

Golgin candidate 6

AT3G27530

Prupe.2G271800

0.769

1

Up_O1

RAS-RELATED PROTEIN RABD2B-RELATED

AT5G47200

Prupe.1G555300

1

6

Up_O1

PATELLIN-3-RELATED

AT1G72160

Prupe.8G192300

1

1

Up_O1

Ras-related protein Rab-11A (RAB11A)

AT3G07410

Prupe.6G024700

0.999

2

Up_O1

Transmembrane emp24 domain-containing protein p24beta2

AT3G07680

 Vesicles Trafficking/Redox Metabolism

Prupe.6G134600

1

2

Up_O1

VESICLE-ASSOCIATED MEMBRANE PROTEIN 714

AT5G22360

 Abiotic Stress

Prupe.3G078100

0.998

2

Up_O2

Chaperone protein DnaJ

AT2G22360

Prupe.2G178200

1

4

Up_O2

DESICCATION-RELATED PROTEIN LEA14-RELATED

AT1G01470

Prupe.7G125900

0.769

1

Up_O2

Aquaporin TIP1-1

AT2G36830

 Anthocyanin transport

Prupe.4G111700

0.998

2

Up_O2

GLUTATHIONE S-TRANSFERASE OMEGA-LIKE 1-RELATED

AT4G19880

 Carbohydrates Metabolism

Prupe.6G210900

0.414

0

Up_O2

phosphoenolpyruvate carboxykinase (ATP) (E4.1.1.49, pckA)

AT4G37870

 Carbohydrates/Energy Metabolism

Prupe.1G105800

0.118

0

Qualit_O2

[Pyruvate dehydrogenase (acetyl-transferring)] kinase / Pyruvate dehydrogenase kinase (phosphorylating)

AT3G06483

YES

 Cargo Delivery into the Peroxisome

Prupe.6G036900

1

3

Qualit_O2

peroxin-5 (PEX5, PXR1)

AT5G56290

 Carotenoid Biosynthetic Process

Prupe.6G340000

1

10

Up_O2

Zeta-carotene desaturase, chloroplastic/chromoplastic

AT3G04870

 Cell Wall Metabolism

Prupe.4G262200

0.598

1

Qualit_O2

Polygalacturonase (PpPG22)

AT3G59850

Prupe.4G261900

0.747

1

Up_O2

Polygalacturonase (PpPG21)

AT3G59850

Prupe.2G300900

0.99

1

Qualit_O2

Probable polygalacturonase

AT3G48950

Prupe.3G050200

1

3

Up_O2

BETA-GALACTOSIDASE 1

AT3G13750

Prupe.5G131300

0.977

1

Up_O2

ENDO-1,4-BETA-GLUCANASE PpEG1

AT1G02800

Prupe.6G075100

0.995

1

Up_O2

Expansin 3 (PpExp3)

AT2G39700

Prupe.4G157600

0.474

0

Up_O2

PROTEIN TRICHOME BIREFRINGENCE-LIKE 41

AT3G14850

Prupe.1G114500

0.745

1

Up_O2

Plant invertase/pectin methylesterase inhibitor (PMEI)

AT1G47960

 Chloroplast Division

Prupe.4G013700

0.5

1

Up_O2

Tetratricopeptide repeat protein 1

AT1G62390

 Endocytosis

Prupe.6G275500

0.998

2

Up_O2

CLATHRIN LIGHT CHAIN 2

AT3G51890

 Energy Metabolism

Prupe.6G244100

1

3

Up_O2

ADENYLATE KINASE 1, MITOCHONDRIAL-RELATED

AT2G37250

Prupe.3G092100

0.998

2

Up_O2

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

AT4G02580

Prupe.6G249900

1

7

Up_O2

INORGANIC PYROPHOSPHATASE-LIKE PROTEIN

AT3G53620

 Hormones Metabolism

Prupe.3G209900

0.643

1

Up_O2

1-aminocyclopropane-1-carboxylate oxidase (ACO1)

AT1G05010

Prupe.1G111900

0.996

1

Up_O2

GIBBERELLIN 2-BETA-DIOXYGENASE 4

AT1G02400

YES

Prupe.7G188800

1

2

Up_O2

2-OXOGLUTARATE (2OG) AND FE(II)-DEPENDENT OXYGENASE-LIKE PROTEIN

AT1G14130

 Lactones biosynthesis

Prupe.6G192200

0.244

0

Qualit_O2

SERINE/THREONINE-PROTEIN KINASE SRK2C

AT1G78290

YES

 Lipids Metabolism

Prupe.7G076500

0.998

2

Qualit_O2

Omega-6 fatty acid desaturase, endoplasmic reticulum isozyme 2

AT3G12120

YES

 Lipids/Hormones Metabolism

Prupe.1G332000

0.769

1

Qualit_O2

Probable peroxygenase 4

AT1G70670

YES

 Lipids Metabolism/Signaling

Prupe.4G089300

1

2

Up_O2

GLYCOLIPID TRANSFER PROTEIN-RELATED

AT2G34690

 MicroRNAs processing

Prupe.6G153800

0.5

1

Up_O2

ARSENITE-RESISTANCE PROTEIN 2

AT2G27100

 Mitotic Cell Cycle Progression

Prupe.1G154700

0.503

1

Up_O2

RAN GTPase-activating protein 2

AT5G19320

 Nuclear Morphology and Heterochromatin Organization

Prupe.6G214100

0.621

1

Qualit_O2

Putative nuclear matrix constituent protein 1-like protein

AT5G65770

 Protein Degradation/Signaling

Prupe.1G040200

0.383

0

Qualit_O2

E3 UBIQUITIN-PROTEIN LIGASE XBAT35-RELATED

AT3G23280

Prupe.7G170300

1

4

Up_O2

26S proteasome regulatory subunit N10 (PSMD4, RPN10)

AT4G38630

 Protein Folding

Prupe.1G348800

0.745

1

Up_O2

prefoldin alpha subunit (pfdA, PFDN5)

AT5G23290

Prupe.1G118100

0.655

0

Up_O2

Peptidyl-prolyl cis-trans isomerase CYP21-3, mitochondrial

AT3G66654

 Protein Synthesis

Prupe.7G265100

1

11

Up_O2

EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA

AT5G57870

Prupe.1G274500

0.998

2

Up_O2

Large subunit ribosomal protein L34e

AT1G26880

Prupe.5G147500

1

4

Up_O2

Large subunit ribosomal protein L7Ae (RP-L7Ae, RPL7A)

AT3G62870

Prupe.6G192100

0.564

1

Up_O2

Small subunit ribosomal protein S6e (RP-S6e, RPS6)

AT5G10360

Prupe.7G268100

1

3

Up_O2

Small subunit ribosomal protein S24e (RP-S24e, RPS24)

AT5G28060

 Protein Targeting

Prupe.7G179600

0.227

0

Up_O2

PROTEIN GLUTAMINE DUMPER 7

AT5G66030

Prupe.1G362200

1

5

Up_O2

Early endosome antigen 1

AT1G20110

 Protein Transport

Prupe.5G110100

0.998

2

Up_O2

RETICULON-LIKE PROTEIN B4

AT4G11220

 Regulation of Transcription

Prupe.1G054700

0.5

1

Qualit_O2

STRUCTURAL MAINTENANCE OF CHROMOSOMES SMC FAMILY MEMBER

AT3G23980

Prupe.8G189400

0.368

0

Up_O2

DnaJ homolog subfamily C member 2 (DNAJC2)

AT3G11450

 Regulation of Translation

Prupe.6G360600

0.567

0

Qualit_O2

PROTEIN PHOSPHATASE RELATED

AT3G02830

 RNA Splicing

Prupe.4G042600

0.101

0

Qualit_O2

splicing factor 3B subunit 2 (SF3B2, SAP145, CUS1)

AT4G21660

Prupe.7G153200

0.23

0

Up_O2

U1 small nuclear ribonucleoprotein 70kDa (SNRP70)

AT3G50670

Prupe.8G029000

0.5

1

Up_O2

ATP-dependent RNA helicase DDX23/PRP28 (DDX23, PRP28)

AT2G33730

Prupe.6G190500

0.536

0

Qualit_O2

SNW domain-containing protein 1 (SNW1, SKIIP, SKIP)

AT1G77180

Prupe.6G349400

0.564

1

Up_O2

Cell division cycle 5-like protein

AT1G09770

 RNA-mediated Post-transcriptional Gene Silencing

Prupe.6G115400

0.395

0

Up_O2

Protein argonaute 5

AT2G27880

 Senescence

Prupe.7G173400

0.5

1

Up_O2

LA-RELATED PROTEIN 1B-RELATED

AT4G35890

 Signaling

Prupe.4G021300

0.571

1

Up_O2

CALCIUM-DEPENDENT PROTEIN KINASE 29

AT4G04720

Prupe.8G057600

0.567

1

Up_O2

SERINE/THREONINE-PROTEIN KINASE

AT4G09570

Prupe.2G134200

0.998

2

Up_O2

Nuclear pore glycoprotein p62

AT2G45000

 Sugar Transport

Prupe.8G101200

0.998

2

Up_O2

POLYOL TRANSPORTER 5 PePOL5

AT3G18830

 Specialized Metabolsim

Prupe.5G106300

0.772

1

Up_O2

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECDP-synthase

AT1G63970

Prupe.8G032700

0.607

1

Up_O2

Sterol 3-beta-glucosyltransferase

AT1G43620

Prupe.3G097700

0.5

1

Up_O2

cinnamoyl-CoA reductase (CCR)

AT1G15950

 Vacuolar Sorting

Prupe.7G171800

0.5

1

Up_O2

VACUOLAR SORTING PROTEIN 35

AT2G17790

Prupe.8G143700

0.607

1

Up_O2

Vacuolar-sorting receptor 3

AT2G14740