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8 recordsLinked to original sources
PubMed2026

Temporal DIA-MS proteomics reveals coordinated metabolic reprogramming associated with oil accumulation in oil palm mesocarp.

Oil palm (Elaeis guineensis Jacq.) is the most productive oil-bearing crop globally, yet the molecular basis of mesocarp development and lipid accumulation remains poorly understood. Ultra-deep data-independent acquisition mass spectrometry (DIA-MS) was applied to characterize proteome dynamics in two contrasting genotypes, seedless (KS) and thin-shelled (TS), across five developmental stages (P1-P5) spanning fruit development to mature oil accumulation. Phenotypic analysis revealed higher mesocarp proportion and oil content in KS during late maturation. A total of 137,615 peptides corresponding to 12,163 protein groups were identified, providing a temporal proteomic landscape of mesocarp development. Multivariate analysis indicated that developmental progression was the primary contributor to proteomic variation, whereas genotype-associated differences increased during lipid accumulation. Differentially abundant proteins were mainly associated with carbohydrate metabolism, photosynthesis, proteolysis, antioxidant responses, and lipid biosynthesis. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and KOG analyses suggested extensive remodeling of metabolic networks, including developmental changes in photosynthesis-associated proteins and increased representation of lipid-associated pathways during maturation. Weighted protein co-expression network analysis identified 17 modules associated with developmental progression and lipid accumulation, highlighting candidate proteins involved in carbon metabolism, energy production, and cellular protection. Genes encoding selected hub protein candidates were further examined by RT-qPCR. Biochemical analyses supported these proteomic patterns, showing increased acetyl-CoA availability, enhanced antioxidant enzyme activities (SOD, CAT, APX, and GR), improved GSH/GSSG balance, and reduced oxidative damage in KS. Together, these findings provide a temporal proteomic and biochemical framework for understanding genotype-associated differences in oil accumulation and identify candidate metabolic networks for functional studies.

Carbon metabolism↗
PubMed2025

SpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package.

SUMMARY: Proteome studies frequently encounter challenges in down-stream data analysis due to limited bioinformatics resources, rapid data generation, and variations in analytical methods. To address these issues, we developed SpectroPipeR, an R package designed to streamline data analysis tasks and provide a comprehensive, standardized pipeline for Spectronaut® DIA-MS data. This novel package automates various analytical processes, including XIC plots, ID rate summary, normalization, batch and covariate adjustment, relative protein quantification, multivariate analysis, and statistical analysis, while generating interactive HTML reports for e.g. ELN systems. AVAILABILITY AND IMPLEMENTATION: The SpectroPipeR package (manual: https://stemicha.github.io/SpectroPipeR/) was written in R and is freely available on GitHub (https://github.com/stemicha/SpectroPipeR).

Software↗
PubMed2026

A porcine spectral assay library to quantify brain proteome by DIA-MS.

Neurological disorders are the leading cause of health loss worldwide. The growing number of patients suffering from such conditions calls for improved strategies for their prevention, diagnosis, and therapy. To better understand human pathologies, relevant models and methodologies must be made available. In this study, we focused on a biomedical model capable of recapitulating the complexity of human pathology, the pig (Sus scrofa). Brain tissue and cerebrospinal fluid samples from a transgenic minipig model of Huntington's disease were subjected to multiple extraction and fractionation steps. A proteomic mass spectrometry (MS) methodology then allowed the generation of a porcine spectral library for 8,321 proteins. Using data-independent acquisition (DIA), we demonstrated that our porcine spectral library substantially enhanced the quantitative potential of this untargeted MS approach, generating reproducible proteome-wide data. The porcine library also provides a comprehensive resource for the development of targeted MS assays, enabling the quantification of selected proteins with a key role not only in neuroscience.

Animals↗
PubMed2026

Saliva and salivary pellicle composition and proteomic profile in smokers vs. non-smokers and its effect on dental erosion.

OBJECTIVE: To analyse the salivary composition and proteomic profile of saliva and the salivary pellicle in smokers compared to non-smokers, and to examine potential differences in the erosion-protective capacity of the salivary pellicle. METHODS: Twenty-five smokers and 25 non-smokers were included. Unstimulated and stimulated saliva samples were analysed regarding flow rate, pH, buffer capacity, calcium, phosphate, fluoride, and protein content. Saliva and salivary pellicle samples were analysed by data-independent acquisition mass spectrometry (DIA-MS) for proteome profiling. In an in situ experiment, intraoral splints were loaded with bovine enamel and dentine specimens for 120 min. Pellicle-covered specimens were extraorally eroded (HCl, pH 2.3, 60 s). Calcium release was determined photometrically and compared to pellicle-free controls. RESULTS: Except for phosphate in stimulated saliva (padj.=0.003), salivary parameters were not significantly different between smokers and non-smokers. Proteome profiling detected 1759±154 proteins (cumulative 1963) in saliva, and 4262±362 proteins (cumulative 4625) in the salivary pellicle. The relative abundances of 282 (unstimulated saliva), 338 (stimulated saliva), and 4 (salivary pellicle) protein groups differed significantly between smokers and non-smokers. Functional enrichment analysis of differentially abundant human proteins revealed biological processes such as coagulation, immune response, and carcinogenic reactive oxygen species processes to be impacted by smoking. The salivary pellicle had a significant erosion-protective effect in enamel compared to the control (41.4 ± 6.3 nmol/mm2), but no differences between smokers (33.2 ± 10.6 nmol/mm2, padj.=0.001) and non-smokers (32.7 ± 8.6 nmol/mm2, padj.=0.001) were found. CONCLUSION: The proteomic profiles of both unstimulated and stimulated saliva and the salivary pellicle differ between smokers and non-smokers. CLINICAL SIGNIFICANCE: Despite the different proteomic profiles indicating a significant impact of smoking on the oral cavity, the erosion-protective capacity of the salivary pellicle of smokers and non-smokers does not differ.

Dental Pellicle↗
PubMed2026

Hyperlactate-Associated Lysine Lactylome Remodeling in Laryngeal Squamous Cell Carcinoma.

Laryngeal squamous cell carcinoma (LSCC) lacks reliable biomarkers, and the roles of lactate metabolism and lysine lactylation (Kla) remain largely unknown. We profiled the lysine lactylome of LSCC, paired it with adjacent normal tissues, and integrated the data with quantitative proteomic and transcriptomic analyses. LSCC exhibited a hyperlactate-associated phenotype characterized by dysregulated lactate-related genes (LRGs), altered protein abundance, increased tissue lactate, and globally increased Kla levels. Data-independent acquisition mass spectrometry (DIA-MS) identified 1616 Kla sites on 1468 peptides from 688 proteins, with most differential sites being upregulated in tumors. Differentially lactylated proteins were enriched in cell-matrix adhesion, cell migration, chromatin remodeling, and gene-regulatory processes and were clustered into cytoskeletal and nuclear regulatory modules. Multiple Kla sites were also detected on the core histones. Immunoblotting and tissue microarray analyses confirmed increased pan-Kla expression in the LSCC. Pan-Kla levels were independent of sex and age but positively correlated with the tumor stage and lymph-node metastasis. These findings provide a systematic resource for hyperlactate-associated lactylome remodeling in LSCCs and identify candidate Kla-related molecular features associated with clinicopathological progression for future functional and clinical evaluation.

Humans↗
PubMed2025

A Study on Differential Proteomics in Differentiated Gastric Adenocarcinoma With Low-grade Atypia Based on Paraffin-embedded Tissues.

In this study, we analyzed and characterized differentially expressed proteins in differentiated gastric adenocarcinoma with low-grade atypia for screening potential protein markers. We collected gastric tissue specimens from 90 patients treated at the Pathology Department of the First People's Hospital of Yunnan Province, China, between January 2019 and December 2022. These specimens had been fixed in 10% neutral-buffered formalin and embedded in paraffin. We classified these samples into 3 groups: the control group (normal gastric mucosa), the low-grade atypia group (differentiated gastric adenocarcinoma with low-grade atypia), and the high-grade atypia group (differentiated gastric adenocarcinoma with high-grade atypia), consisting of 30 cases in each group. We analyzed differential proteomes with the data-independent acquisition-mass spectrometry (DIA-MS) methodology and selected 4 differentially expressed proteins that were subjected to immunohistochemistry (IHC) staining for validation. A total of 4406 proteins were identified, among which 598 and 357 proteins were statistically different in the low-grade atypia group as compared with the control group and the high-grade atypia group, respectively. IHC staining showed that the expression of FHL3, CSRP2, and FCGR3A was significantly higher in the low-grade atypia group than in the control group ( P <0.05) and significantly higher in the high-grade atypia group than in the low-grade atypia group ( P <0.05). FHL2 expression was negative to weakly positive in the control and low-grade atypia groups and not significantly different between the 2 groups, whereas FHL2 expression in the high-grade atypia group was significantly higher than in the control and low-grade atypia groups ( P <0.05). Proteomic analysis is helpful for discovering new protein markers. Using a combination of FHL3, CSRP2, and FCGR3A can increase the accuracy of the pathologic diagnosis of differentiated gastric adenocarcinoma with low-grade atypia.

Humans↗
PubMed2025

Widespread release of translational repression across Plasmodium's host-to-vector transmission event.

Malaria parasites must respond quickly to environmental changes, including during their transmission between mammalian and mosquito hosts. Therefore, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. While the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, changes in the spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we found that ~200 transcripts are released for translation soon after fertilization, including those encoding essential functions. Moreover, we identified that many transcripts remain repressed beyond this point. TurboID-based proximity proteomics of the DOZI/CITH/ALBA regulatory complex revealed substantial spatial and/or compositional changes across this transmission event, which are consistent with recent, paradigm-shifting models of translational control. Together, these data provide a model for the essential translational control mechanisms that promote Plasmodium's efficient transmission from mammalian host to mosquito vector.

Animals↗
PubMed2026

Plasma Proteomic Profiling of Comorbid and Noncomorbid COVID-19 Patients in ICU.

Type 2 Diabetes (T2D) and hypertension (HTN) are common comorbidities in severe COVID-19, yet their specific impact on proteomic recovery remains unclear. This study analyzed plasma protein signatures of critical COVID-19 patients with and without these comorbidities (COVID-only group [COG] and COVID comorbid group [CTHG]) on the first and last days of ICU stay. Proteomic analysis revealed a systemic shift characterized by upregulated immune responses and downregulated metabolic processes at admission across all patients. Survival was fundamentally defined by the restoration of homeostasis; liver-derived proteins&#x2500;including LPA, TTR, and AHSG&#x2500;were initially suppressed but rebounded significantly in survivors. This homeostatic recovery was impaired in CTHG compared to COG, with CTHG survivors showing attenuated recovery of metabolic markers. Distinct mortality-associated signatures also emerged between groups. COG nonsurvivors exhibited liver failure and severe hemolysis marked by persistent suppression of haptoglobin (HP). In contrast, CTHG mortality was driven by lipid metabolism dysregulation, with CD5L and APOA2 levels dropping specifically in comorbid nonsurvivors, often accompanied by a paradoxical elevation in APOA4&#x2500;likely reflecting impaired renal clearance rather than restored lipid homeostasis. These findings indicate that preexisting T2D and HTN hinder physiological resolution of metabolic and lipid dysregulation, providing proteomic evidence for distinct mortality risks associated with failure to restore metabolic homeostasis in comorbid COVID-19 patients.

Humans↗