Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species
Abstract
:1. Introduction
2. Results
2.1. Variation in Organic Acid and Soluble Sugar Contents in the Mature Fruits of Two Wild Apple Species
2.2. Quality and Coverage of the Apple Fruit Proteome
2.3. Verification of the Differentially Expressed Proteins by PRM
2.4. Analysis of Differentially-Expressed Proteins Based on the gene ontology (GO) and KEGG Databases
2.5. Specificity of the Protein Accumulation Related to Soluble Sugar and Organic Acid Metabolism
2.6. Identification of Proteins Involved in H+ transport
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Determination of Soluble Sugar and Organic Acid Contents
4.3. Protein Extraction, Enzymatic Hydrolysis, and Peptide Quantification
4.4. Data Analysis
4.5. Bioinformatic Analysis
4.6. PRM Verification
Supplementary Materials
Data Archiving Statement
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Identification Results | Unique Peptides | Quantified Proteins | Msa vs. Mni | Significantly Different Proteins | |
---|---|---|---|---|---|
Up-Regulated | Down-Regulated | ||||
Total | 13036 | 2901 | 416 | 663 | 1079 |
Peptide Sequence | Protein Name | Average Content | PRM Fold Change | Label-Free Fold Change | Consistency between PRM and Label-Free | |
---|---|---|---|---|---|---|
Msa | Mni | |||||
EYYTNALAAAK | MDP0000271088 | 0.0127 | 0.1152 | 0.1106 | 0.7260 | Yes |
VSLGNFPDLAGAVNK | ||||||
FLVSDSFPGNDR | MDP0000152497 | 0.6065 | 0.7086 | 0.8559 | 0.3358 | Yes |
LVPIINPTTR | ||||||
INDQAGYSSFR | MDP0000326249 | 0.4397 | 0.0483 | 9.1035 | 2.9726 | Yes |
LANILHANELAR | ||||||
ANEAALDLVR | MDP0000777702 | 0.3039 | / | _ | _ | Yes |
YNEGALPGFDPATK | ||||||
AFVDSGAQSTIISK | MDP0000308185 | / | 0.2294 | _ | _ | Yes |
GIAHGVGQSEILGR | ||||||
LVELGFGR |
Item | Value |
---|---|
Enzyme | Trypsin |
Max missed cleavages | 2 |
Max missed cleavages | 2 |
Main search | 6 ppm |
First search | 20 ppm |
MS/MS tolerance | 20 ppm |
Fixed modifications | Carbamidomethyl (C) |
Variable modifications | Oxidation (M), acetyl (protein N-term) |
Peptide FDR | ≤0.01 |
Protein FDR | ≤0.01 |
Time window (match between runs) | 2 min |
Protein quantification | Razor and unique peptides were used for protein quantification. |
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Ma, B.; Ding, Y.; Li, C.; Li, M.; Ma, F.; Yuan, Y. Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species. Plants 2019, 8, 488. https://doi.org/10.3390/plants8110488
Ma B, Ding Y, Li C, Li M, Ma F, Yuan Y. Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species. Plants. 2019; 8(11):488. https://doi.org/10.3390/plants8110488
Chicago/Turabian StyleMa, Baiquan, Yuduan Ding, Cuiying Li, Mingjun Li, Fengwang Ma, and Yangyang Yuan. 2019. "Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species" Plants 8, no. 11: 488. https://doi.org/10.3390/plants8110488