Dataset Information

Tomato fruit ripening Phosphoproteome

ABSTRACT: Through the quantitative proteomics research strategy of TMT labeling and phosphorylation enrichment technology and high-resolution liquid chromatography-mass spectrometry, this project carried out the quantitative research of phosphorylated proteomics. In this study, a total of 6227 phosphorylation sites were identified, of which 4501 sites contained quantitative information. In order to ensure the high reliability of the results, we used the standard of localization probability>0.75 to filter the identification data, and finally determined 4842 phosphorylation sites located on 2328 proteins, of which 4,011 sites of 1996 proteins contained quantitative Information, and use the filtered data for subsequent bioinformatics analysis. If 1.5 times is the change threshold, t-test p-value<0.05 is the standard, and after full proteomics normalization, then among the quantified phosphorylation sites, there are 161 in the AC-B4vsAC-MG comparison group The modification level of the locus was up-regulated, and the modification level of 364 sites was down-regulated (for more information about the differences between the comparison groups, please see the main body of the report). Based on the above data, we conducted a systematic bioinformatics analysis of proteins containing quantitative information, including protein annotation, functional classification, functional enrichment, and cluster analysis based on functional enrichment. And combining the above information provides a reference direction for the downstream in-depth research based on proteomics.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Solanum Lycopersicum

TISSUE(S): Pericarp

SUBMITTER: Qiaoli Xie

LAB HEAD: Qiaoli Xie

PROVIDER: PXD027844 | Pride | 2022-02-17

REPOSITORIES: Pride

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Publications

Novel Translational and Phosphorylation Modification Regulation Mechanisms of Tomato (Solanum lycopersicum) Fruit Ripening Revealed by Integrative Proteomics and Phosphoproteomics.

Xie Qiaoli Q Tian Yanling Y Hu Zongli Z Zhang Lincheng L Tang Boyan B Wang Yunshu Y Li Jing J Chen Guoping G

International journal of molecular sciences 20211029 21

The tomato is a research model for fruit-ripening, however, its fruit-ripening mechanism still needs more extensive and in-depth exploration. Here, using TMT and LC-MS, the proteome and phosphoproteome of AC++ (wild type) and rin (ripening-inhibitor) mutant fruits were studied to investigate the translation and post-translational regulation mechanisms of tomato fruit-ripening. A total of 6141 proteins and 4011 phosphorylation sites contained quantitative information. One-hundre ...[more]

PMID: 34769214

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Project description:Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.