Preanalytical Factors Affect Plasma EV and Human Plasma Proteome
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Blood Plasma
SUBMITTER: 
Qibin Zhang
LAB HEAD: Qibin Zhang
PROVIDER: PXD065458 | Pride | 2026-03-30
REPOSITORIES: Pride
Dataset's files
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| 20Years_Storage_1.raw | Raw | |||
| 20Years_Storage_2.raw | Raw | |||
| 20Years_Storage_3.raw | Raw | |||
| 20Years_Storage_4.raw | Raw | |||
| 2Years_Storage_1.raw | Raw |
Items per page: 5 1 - 5 of 34 |
Publications
Impact of preanalytical factors on plasma extracellular vesicles and human plasma proteome.
Suresh Patil Shivprasad PS Zhang Qibin Q
Clinical proteomics 20260221 1
Using human plasma and its protein-rich extracellular vesicles (EVs) for proteomic biomarker discovery requires an in-depth understanding of the influences of pre-analytical procedures. This study systematically investigates the ramifications of high-speed centrifugation, freeze-thaw cycles, and prolonged storage on the plasma proteome and abundance of plasma EVs. Employing a Mag-Net-assisted workflow for high-throughput EV-based plasma proteomics, we find that high-speed centrifuging plasma sam ...[more]
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Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.
2009-08-31 | GSE15461 | GEO
Project description:In frozen dough baking technology, baker’s yeast Saccharomyces cerevisiae encounter freeze-thaw injury. After thawing, dramatically decrease in cell viability and fermentation activity is caused by freeze-thaw injury. The freezing period is critical factor in freeze-thaw injury, thus we focused and investigated time-dependent gene expression profiles in recovery process from freeze injury. First, changes in gene expression profiles in S. cerevisiae in recovery process from freeze-thaw injury were analyzed using a DNA microarray. The results showed the genes which were involved in homeostasis of metal ions were time-dependent up-regulated 2-fold or more in a series. Then we examined whether these genes were related to tolerance in freeze-thaw injury by using deletion strain. The results showed that deletion of MAC1, CTR1, and PCA1 genes which involved in copper ion transport exhibited freeze-thaw sensitivity in compared with wild type. These genes are involved in copper ion uptake to a cell under a copper deficiency condition or in copper ion homeostasis, suggesting that it may be related between freeze-thaw injury and copper ion transport. To determine the effect of supplementation of copper ion on cells after freeze-thaw treatment, cell viability, intracellular superoxide dismutase (SOD) activity, and intracellular levels of reactive oxygen species (ROS) were examined by various copper ion condition medium. The results showed that intracellular SOD activity was increased and intracellular levels of ROS were decreased by supplementation of copper ion, but there was no significant difference in cell viability. These results of the present study may suggest that copper ion concentration in yeast cell after freeze-thaw treatment is important to recovery from freeze-thaw injury due to redox control of intracellular levels of ROS, but copper ion did not directly affect cell viability.
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Project description:Advancements in mass spectrometry and complementary technologies now enable comprehensive and high-resolution plasma proteomics. Plasma is a key biofluid for clinical research, harboring potential disease informative biomarkers. Commercial sources of non-diseased, healthy donor plasma samples are often used for proteomic workflow development and as controls for clinical studies. The overarching assumption is that standard operating procedures for plasma preparations are comparable across variable sources. In this study, we investigated the effectiveness of a particle-based protein enrichment strategy against a conventional proteomics workflow on plasma samples from 5 commonly used sources aiming to characterize the extent of variability when factors such as freeze-thaw cycles, anticoagulant, and operator-to-operator performance were controlled. Plasma samples were analyzed in data-independent acquisition mode using two distinct instruments (Exploris 480, timsTOF HT) and search algorithms (CHIMERYS, DIA-NN). Plasma proteome enrichment yields ranged from 4.5 to 8-fold more compared to the conventional workflow, achieving yields exceeding 5,000 proteins. Notably, the observer variability in proteome composition was largely attributable to differences in whole blood-to-plasma operating procedures across the sources. While these distinct proteomes remained undetectable with conventional workflows, particle-dependent proteome profiling successfully revealed the procedural differences.
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Project description:Frozen dough baking is useful method in the modern bread-making industry. However, the fermentation activity of baker’s yeast dramatically decreased after thawing due to freeze injuries, because baker’s yeast cells contained in dough experience freeze injuries during freeze-thaw processes. Here, we performed genome-wide expression analysis to determine genetic response in baker’s yeasts under freeze-thaw condition using a DNA microarray analysis. Functional and clustering analyses in gene expression reveal that genes could be characterized by the term of freeze-thaw stress. Under short-term freeze stress (freeze treatment for 3 day), genes involved in ribosomal protein were up-regulated. Under long-term freeze stress (freeze treatment for longer than 7 day), genes involved in energy synthesis were up-regulated. In each phase, genes involved in protein damage, several stresses and trehalose and glycogen metabolism were also up-regulated. Through these freeze stress, yeast cells may improve reduced efficiency of translation and enhanced cell protection mechanism to survive under freeze stress condition. These regulations of these genes would be controlled by the cAMP-protein kinase A pathway. Keywords: baker’s yeast, freeze-thaw stress, gene expression, freezing period
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Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury. Total RNA was extracted from the stress-treated yeast cells by using a hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dT30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan). cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA). Biotinyated cRNA was fragmented and then used as a probe.Affimetrix Yeast Genome 2.0 arrays (Affymetrix) were used as DNA microarrays. All experiments were done in triplicate independently.
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Project description:The data submitted is for the proteomics data published in the paper: A systematic evaluation of isolation techniques and freeze-thaw effects on plasma extracellular vesicle heterogeneity and subpopulation profiling
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