Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology

Hashimoto, Yutaka; Greco, Todd M.; Cristea, Ileana M.

doi:10.1007/978-3-030-15950-4_8

Cited by 7 publications

(8 citation statements)

References 138 publications

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“…The methods of protein extraction and trypsin digestion for the PRM analysis were similar to that described for the TMT proteomics. The LC-MS/MS analysis and the data analysis of PRM were performed following the methods described by Hashimoto et al (2019) with some modifications. The tryptic peptides were dissolved in 0.1% formic acid (solvent A) and also loaded onto a reversed-phase analytical column.…”

Section: Prm Validation For Targeted Ms Analysismentioning

confidence: 99%

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

Shen

Xu²,

Qing-yun³

et al. 2022

Front. Plant Sci.

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Quinoa (Chenopodium quinoa Willd.), an Andean native crop, is increasingly popular around the world due to its high nutritional content and stress tolerance. The production and the popularity of this strategic global food are greatly restricted by many limiting factors, such as seed pre-harvest sprouting, bitter saponin, etc. To solve these problems, the underlying mechanism of seed maturation in quinoa needs to be investigated. In this study, based on the investigation of morphological characteristics, a quantitative analysis of its global proteome was conducted using the combinational proteomics of tandem mass tag (TMT) labeling and parallel reaction monitoring (PRM). The proteome changes related to quinoa seed maturation conversion were monitored to aid its genetic improvement. Typical changes of morphological characteristics were discovered during seed maturation, including mean grain diameter, mean grain thickness, mean hundred-grain weight, palea, episperm color, etc. With TMT proteomics analysis, 581 differentially accumulated proteins (DAPs) were identified. Functional classification analysis and Gene Ontology enrichment analysis showed that most DAPs involved in photosynthesis were downregulated, indicating low levels of photosynthesis. DAPs that participated in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase, were upregulated to fulfill the increasing requirement of energy consumption during maturation conversion. The storage proteins, such as globulins, legumins, vicilins, and oleosin, were also increased significantly during maturation conversion. Protein–protein interaction analysis and function annotation revealed that the upregulation of oleosin, oil body-associated proteins, and acyl-coenzyme A oxidase 2 resulted in the accumulation of oil in quinoa seeds. The downregulation of β-amyrin 28-oxidase was observed, indicating the decreasing saponin content, during maturation, which makes the quinoa “sweet”. By the PRM and qRT-PCR analysis, the expression patterns of most selected DAPs were consistent with the result of TMT proteomics. Our study enhanced the understanding of the maturation conversion in quinoa. This might be the first and most important step toward the genetic improvement of quinoa.

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Section: Prm Validation For Targeted Ms Analysismentioning

confidence: 99%

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

Shen

Xu²,

Qing-yun³

et al. 2022

Front. Plant Sci.

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“…Therefore, the development of SCPs provides a new perspective for view the morphological development [23,[26][27][28].…”

Section: Introductionmentioning

confidence: 99%

“…Using SCPs, a recent report reconstructed the developmental trajectory and revealed key proteins during the differentiation of hair cells [25 ]. Therefore, the development of SCPs provides a new perspective for view the morphological development [23, 26–28].…”

Section: Introductionmentioning

confidence: 99%

Proteomic identification of intracellular vesicle trafficking and protein glycosylation requirements for lumen inflation in Ciona notochord

et al. 2023

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Lumen formation and inflation are crucial steps for tubular organ morphogenesis, yet the underling mechanism remains largely unrevealed. Here, we applied 4D proteomics to screen the lumenogenesis‐related proteins and revealed the biological pathways potentially that are involved in lumen inflation during notochord lumen formation in the ascidian Ciona savignyi. In total, 910 differentiated expressed proteins (DEPs) were identified before and after notochord lumen formation utilizing Mfuzz analysis. Those DEPs were grouped into four upregulated clusters based on their quantitative expression patterns; the functions of these proteins were enriched in protein metabolic and biosynthetic process, the establishment of localization, and vesicle‐mediated transport. We analyzed the vesicle trafficking cluster and focused on several vesicle transport hub proteins. In vivo function‐deficient experiments showed that mutation of vesicle transport proteins resulted in an abnormal lumen in notochord development, demonstrating the crucial role of intracellular trafficking for lumen formation. Moreover, abundant extracellular matrix proteins were identified, the majority of which were predicted to be glycosylated proteins. Inhibition of glycosylation markedly reduced the lumen expansion rate in notochord cells, suggesting that protein glycosylation is essential for lumenogenesis. Overall, our study provides an invaluable resource and reveals the crucial mechanisms in lumen formation and expansion.

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“…Current basic and applied research of living systems occurs amid several rapidly evolving scientific paradigms, omics ( e.g. , genomics, transcriptomics, proteomics, and metabolomics), − systems biology, − and synthetic biology, − that influence the researcher to look broadly at the holistic system or organism under study. Propelled by key developments of the Information Age, these scientific paradigms encourage scientists to aim for the comprehensive characterization and quantification of the relevant functional units of a cell, organ, organism, or entire system ( e.g.…”

Section: Introductionmentioning

confidence: 99%

Quantum Chemistry Calculations for Metabolomics

et al. 2021

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A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e. , in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

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Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology

Cited by 7 publications

References 138 publications

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

Proteomic identification of intracellular vesicle trafficking and protein glycosylation requirements for lumen inflation in Ciona notochord

Quantum Chemistry Calculations for Metabolomics

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