DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages
Abstract
:1. Introduction
2. Results
2.1. Overview of Proteomic Profiles
2.2. Analysis of Differential Expression Proteins (DEPs)
2.3. Functional Annotation Analysis of Differential Expression Proteins (DEPs)
2.4. Weighted Gene Co-Expression Network Analysis (WGCNA)
3. Discussion
3.1. DEPs Involved in Protein Synthesis
3.2. DEPs Involved in Carbohydrate and Energy Metabolism
3.3. DEPs Involved in Other Metabolism
4. Materials and Methods
4.1. Plant Materials
4.2. Protein Preparation and Digestion
4.3. Filter-Aided Sample Preparation (FASP Digestion) Procedure
4.4. Data Dependent Acquisition (DDA) Mass Spectrometry Assay
4.5. Data Independent Acquisition (DIA) Mass Spectrometry Assay
4.6. Mass Spectrometry Data Analysis
4.7. Bioinformatic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Protein ID | Description | HC1 vs. GL1 | HC2 vs. GL2 | HC3 vs. GL3 |
---|---|---|---|---|
A0A498JQC8 | Glyceraldehyde-3-phosphate dehydrogenase | 2.13 | 2.24 | 3.01 |
A0A540KTG1 | Glyceraldehyde-3-phosphate dehydrogenase | 1.99 | - | 2.38 |
A0A540M707 | Probable 6-phosphogluconolactonase | 1.78 | 1.87 | - |
A0A498I8M1 | Malate dehydrogenase | 1.61 | - | 1.94 |
A0A498JSH1 | Phosphopyruvate hydratase | 0.04 | - | - |
A0A540KR11 | ATP citrate synthase | - | 1.86 | 2.48 |
A0A540MIX1 | Pyrophosphate--fructose 6-phosphate 1-phosphotransferase subunit beta | - | 1.69 | 1.72 |
Q9ZPB7 | Aldehyde dehydrogenase family 7 member A1 | - | 1.62 | - |
A0A540NAK7 | Pyruvate kinase | - | 0.63 | - |
A0A498ITD4 | Glucose-6-phosphate dehydrogenase (NADP(+)) | - | 0.60 | - |
A0A1B1UZZ5 | Phosphoenolpyruvate carboxykinase | - | 0.60 | - |
A0A498HRZ9 | Glucose-6-phosphate 1-dehydrogenase | 0.60 | ||
A0A498I194 | Aldedh domain-containing protein | - | 0.57 | - |
A0A498KGN9 | Succinate dehydrogenase | - | 0.57 | - |
A0A498HDN1 | Succinate dehydrogenase | - | 0.56 | - |
A0A540NBC6 | Citrate synthase | - | 0.55 | - |
A0A540LJY9 | Glucose-6-phosphate isomerase | - | 0.53 | - |
A0A498HE04 | Citrate synthase | - | 0.52 | - |
A0A498HN15 | ATP citrate synthase | - | 0.51 | - |
A0A498JRL5 | Phosphoglycerate kinase | - | 0.49 | - |
A0A498KQA5 | ATP-dependent 6-phosphofructokinase | - | 0.47 | - |
A0A540M0H0 | ATP-dependent 6-phosphofructokinase | - | 0.45 | - |
A0A498JVZ3 | Fructose-bisphosphate aldolase | - | 0.41 | - |
A0A498J4J5 | Glucose-6-phosphate 1-dehydrogenase | - | 0.39 | - |
A0A498KN40 | Phosphopyruvate hydratase | - | - | 3.03 |
A0A498IKR9 | Pyruvate kinase | - | - | 2.08 |
A0A540M4P5 | Aldehyde dehydrogenase (NAD(+)) | - | - | 2.05 |
A0A498IVM7 | Pyruvate decarboxylase | - | - | 1.97 |
A0A498K862 | Pyruvate kinase | - | - | 1.71 |
A0A498JT62 | Pyrophosphate--fructose 6-phosphate 1-phosphotransferase subunit alpha | - | - | 1.64 |
A0A498HK68 | Aldose 1-epimerase | - | - | 0.54 |
A0A498JQT3 | Pyruvate kinase | - | - | 0.54 |
A0A498K2Y9 | Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex | - | - | 0.51 |
Protein ID | Description | HC1 vs. GL1 | HC2 vs. GL2 | HC3 vs. GL3 |
---|---|---|---|---|
A0A498HTE9 | Ectonucleotide pyrophosphatase/phosphodiesterase family member 1/3 | 2.22 | - | 4.25 |
A0A498KGZ1 | UTP--glucose-1-phosphate uridylyltransferase | 0.63 | - | 0.57 |
A0A540L083 | Glucose-1-phosphate adenylyltransferase | 0.56 | 0.25 | - |
A0A498JZZ9 | Trehalose 6-phosphate synthase | - | 1.98 | |
A0A498INN2 | β-glucosidase | - | 1.85 | |
A0A498IVD8 | Glycogen phosphorylase | - | 1.58 | |
A0A498KD22 | β-glucosidase | - | 1.51 | |
A0A498JB71 | Alpha-amylase | - | 0.67 | |
A0A498ITV5 | Glucan endo-1,3-beta-D-glucosidase | - | 0.66 | |
A0A498J394 | “Alpha-1,4 glucan phosphorylase” | - | 0.66 | |
A0A498JBU0 | Granule-bound starch synthase | - | 0.59 | |
A0A540K631 | UTP--glucose-1-phosphate uridylyltransferase | - | 0.56 | |
A0A540LJY9 | Glucose-6-phosphate isomerase | - | 0.53 | |
A0A498K3I6 | Alpha-amylase | - | 0.51 | |
A0A498HCN5 | “Alpha-1,4 glucan phosphorylase” | - | 0.47 | |
A0A498IMZ2 | β-glucosidase | - | 0.45 | |
A0A540KIV9 | Sucrose-phosphate synthase | - | 0.39 | |
A0A498KQ57 | Beta-fructofuranosidase | - | 0.38 | |
A0A498JFR5 | Beta-amylase | - | 7.8 | |
B2LUN5 | “Starch synthase, chloroplastic/amyloplastic” | - | 3.76 | |
A0A498HVP0 | Sucrose synthase | - | 2.62 | |
A0A498KKD2 | Sucrose synthase | - | 2.24 | |
A0A498KD22 | “Alpha-1,4 glucan phosphorylase” | - | 2.24 | |
A0A498IFG9 | Amylomaltase | - | 2.05 | |
A0A498J394 | “Alpha-1,4 glucan phosphorylase” | - | 1.74 | |
A0A498JXG5 | Glucose-1-phosphate adenylyltransferase | - | 1.72 | |
A0A498HMG6 | Glyco_transf_20 domain-containing protein | - | 1.71 | |
A0A498J684 | Glucose-1-phosphate adenylyltransferase | - | 1.67 | |
A0A498HLR5 | Endoglucanase | - | 0.52 | |
A0A498IIV3 | β-glucosidase | - | 0.46 |
Protein ID | Description | HC1 vs. GL1 | HC2 vs. GL2 | HC3 vs. GL3 |
---|---|---|---|---|
A0A498HR73 | NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit 10 | 2.65 | - | - |
A0A540L321 | NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit 10 | 1.62 | - | - |
A0A498JWZ4 | Inorganic diphosphatase | 0.66 | - | - |
A0A498HS84 | Cytochrome b-c1 complex subunit 6 | 0.65 | - | - |
A0A498KI10 | “NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial” | 0.65 | - | - |
A0A498HIN9 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 13 | 0.64 | - | 0.43 |
A0A540KHW1 | Cytochrome c oxidase subunit 5b | 0.61 | - | - |
A0A1C8YB78 | “ATP synthase subunit b, chloroplastic” | - | 0.66 | - |
A0A0U2PCG6 | NADH dehydrogenase subunit 7 | - | 0.65 | - |
A0A540K7R9 | NADH dehydrogenase (ubiquinone) Fe-S protein 8 | - | 0.65 | - |
A0A0U2N8T4 | ATP synthase subunit alpha | - | 0.63 | - |
A0A540LIW9 | L51_S25_CI-B8 domain-containing protein | - | 0.63 | - |
A0A498IGB9 | CHCH domain-containing protein | - | 0.61 | - |
A0A498K1S4 | NADH dehydrogenase (ubiquinone) Fe-S protein 8 | - | 0.58 | - |
A0A498KGN9 | “Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial” | - | 0.57 | - |
A0A540LA69 | Ubiquinol-cytochrome c reductase subunit 9 | - | 0.57 | - |
A0A498HDN1 | “Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial” | - | 0.56 | - |
A0A540KIA4 | Cytochrome b-c1 complex subunit 7 | - | 0.53 | - |
A0A540M5Y1 | Acyl carrier protein | - | 0.53 | - |
A0A498IPL8 | Complex I-B22 | - | 0.51 | - |
A0A498HTR2 | “NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial” | - | 0.49 | - |
A0A498HI08 | Cytochrome c oxidase subunit 5b | - | 0.45 | - |
A0A498HA14 | F-type H+-transporting ATPase subunit epsilon | - | 0.38 | - |
A0A498HSD4 | “NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial” | - | 0.36 | - |
A0A498KJ40 | F-type H+-transporting ATPase subunit O | - | 0.20 | - |
A0A498J104 | Plasma membrane ATPase | - | - | 1.85 |
A0A498IJL8 | H(+)-exporting diphosphatase | - | - | 1.58 |
A0A498ICJ5 | V-type proton ATPase subunit G | - | - | 0.65 |
A0A498ILV3 | V-tcype proton ATPase subunit F | - | - | 0.65 |
A0A498JAF9 | Cytochrome c oxidase subunit 6b | - | - | 0.65 |
A0A540MXE2 | F-type H+-transporting ATPase subunit O | - | - | 0.62 |
A0A498I904 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 13 | - | - | 0.61 |
A0A498KNH1 | “ATP synthase subunit d, mitochondrial” | - | - | 0.56 |
A0A498KLQ7 | Acyl carrier protein | - | - | 0.46 |
A0A498K7I9 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | - | - | 0.44 |
A0A540LYH9 | Acyl carrier protein | - | - | 0.41 |
A0A540L2D7 | Acyl carrier protein | - | - | 0.38 |
Protein ID | Description | HC1 vs. GL1 | HC2 vs. GL2 | HC3 vs. GL3 |
---|---|---|---|---|
A0A498KCP1 | Peroxidase | 0.46 | 0.37 | - |
A0A498HEU3 | Shikimate O-hydroxycinnamoyltransferase | 0.46 | - | - |
A0A498I2P0 | Peroxidase | 0.43 | 0.50 | - |
A0A540MB71 | 5-O-(4-coumaroyl)-D-quinate 3′-monooxygenase | - | 1.64 | - |
A0A498KKN7 | Peroxidase | - | 1.62 | 2.24 |
H9U3A3 | Cinnamate-4-hydroxylase | - | 0.64 | - |
A0A498IIU4 | Peroxidase | 0.62 | 0.59 | - |
A0A498JXD0 | Caffeoyl-CoA O-methyltransferase | - | 0.38 | - |
A0A498KLW3 | Peroxidase | - | - | 2.10 |
A0A540NF19 | Coniferyl-alcohol glucosyltransferase | - | - | 1.95 |
C5IGQ5 | Flavonoid 3′ hydroxylase IIb | - | - | 0.62 |
A0A498J555 | Fe2OG dioxygenase domain-containing protein | - | - | 0.54 |
A0A498I8Y9 | Caffeoyl-CoA O-methyltransferase | - | - | 0.52 |
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Li, L.; Lu, X.; Dai, P.; Ma, H. DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages. Int. J. Mol. Sci. 2024, 25, 2964. https://doi.org/10.3390/ijms25052964
Li L, Lu X, Dai P, Ma H. DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages. International Journal of Molecular Sciences. 2024; 25(5):2964. https://doi.org/10.3390/ijms25052964
Chicago/Turabian StyleLi, Lijie, Xiaochen Lu, Ping Dai, and Huaiyu Ma. 2024. "DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages" International Journal of Molecular Sciences 25, no. 5: 2964. https://doi.org/10.3390/ijms25052964