Proteomics最新文献

Inferring evolutionary relationships among organisms has been a fundamental problem in evolutionary biology. The current phylogenetic molecular methods serve as the baseline model to test new evolutionary hypotheses with taxonomic purposes. Leishmaniinae trypanosomatids subfamily includes protozoan parasites of clinical importance to humans. They have an intricate taxonomic history defined by morphological elements, host range, and molecular phylogenies. Unraveling the increasing diversity of this group has shown limitations in reconstructing the true evolutionary relationships among Trypanosomatidae species. Toward the goal of inferring evolutionary relationships that help to resolve phylogenetic and taxonomic controversies among parasites of the subfamily Leishmaniinae, Mule et al. propose the method PhyloQuant as a valuable approach, based on differential protein expression obtained from high throughput mass spectrometry data. Employing a pioneering methodological approach, Mule et al. assess the taxonomic problem for species hypothesis within Leishmaniinae, from quantitative phenetic protein expression profiles, in contrast to the standard multilocus phylogenetic approaches.

Arterial thrombosis contributes to some of the most frequent causes of mortality globally, such as myocardial infarction and stroke. Platelets are essential mediators of physiological haemostasis and pathological thrombosis. Platelet activation is controlled by a multitude of signalling pathways. Upon activation, platelets shed platelet-derived extracellular vesicles (pEVs). In this Special Issue: Extracellular Vesicles, Moon et al. investigate the impact of various platelet agonists (thrombin, ADP, collagen) on the proteome of pEVs. The study demonstrates that pEVs exhibit an agonist-dependent altered proteome compared to their parent cells, with significant variations in proteins related to coagulation, complement, and platelet activation. The study observes the rapid generation of pEVs following agonist stimulation with specific proteome alterations that underscore an active packaging process. This commentary highlights the implications of their findings and discusses the role of pEV cargo in cardiovascular disease with potential novel therapeutic and diagnostic opportunities.

Hao, L., Zhou, X., Liu, S., Sun, M., Song, Y., Du, S., Sun, B., Guo, C., Gong, L., Hu, J., Guan, H., Shao, S. (2015). Elevated GAPDH expression is associated with the proliferation and invasion of lung and esophageal squamous cell carcinomas, Proteomics, 15(17), 3087–3100. https://doi.org/10.1002/pmic.201400577

The above article, published online on May 6, 2015 in Wiley Online Library (wileyonlinelibrary.com), and a corresponding correction (https://doi.org/10.1002/pmic.202070084; published May 25, 2020) have been retracted by agreement between the journal Editor-in-Chief, Lucie Kalvodova; and Wiley-VCH GmbH, Weinheim. The retraction has been agreed following concerns raised by the authors; the same shVector panel was used in two of the figures, suggesting the same control data was used for different experiments.

RETRACTION: I. Popova, E. Savelyeva, T. Degtyarevskaya, D. Babaskin, and A. Vokhmintsev, “Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination,” Proteomics 24, no. 14 (2024): 2300351, https://doi.org/10.1002/pmic.202300351.

The above article, published online on 03 May 2024 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Lucie Kalvodova; and Wiley-VCH GmbH. The retraction has been agreed due to a major unattributed overlap between the figures and figure legends of this article (Figures 2–7) and another article previously published elsewhere by a different group of authors [1]. Such publishing practice is against the journal's policy and Wiley's Best Practice Guidelines on Research Integrity and Publishing Ethics. The co-authors, I. Popova, T. Degtyarevskaya, D. Babaskin, and A. Vokhmintsev stated that they did not participate in the writing and submission of the article and gave no consent for publication. E. Savelyeva remained unresponsive.

REFERENCES

1. H. Boekweg, A. J. Guise, E. D. Plowey, R. T. Kelly, and S. Payne, “Calculating Sample Size Requirements for Temporal Dynamics in Single-Cell Proteomics,” Molecular & Cellular Proteomics 20, (2021): 100085, https://doi.org/10.1016/j.mcpro.2021.100085.

State-of-the-art mass spectrometers combined with modern bioinformatics algorithms for peptide-to-spectrum matching (PSM) with robust statistical scoring allow for more variable features (i.e., post-translational modifications) being reliably identified from (tandem-) mass spectrometry data, often without the need for biochemical enrichment. Semi-specific proteome searches, that enforce a theoretical enzymatic digestion to solely the N- or C-terminal end, allow to identify of native protein termini or those arising from endogenous proteolytic activity (also referred to as “neo-N-termini” analysis or “N-terminomics”). Nevertheless, deriving biological meaning from these search outputs can be challenging in terms of data mining and analysis. Thus, we introduce TermineR, a data analysis approach for the (1) annotation of peptides according to their enzymatic cleavage specificity and known protein processing features, (2) differential abundance and enrichment analysis of N-terminal sequence patterns, and (3) visualization of neo-N-termini location. We illustrate the use of TermineR by applying it to tandem mass tag (TMT)-based proteomics data of a mouse model of polycystic kidney disease, and assess the semi-specific searches for biological interpretation of cleavage events and the variable contribution of proteolytic products to general protein abundance. The TermineR approach and example data are available as an R package at https://github.com/MiguelCos/TermineR.

INS^C94Y transgenic pigs represent a model for mutant insulin gene-induced diabetes of youth, with impaired insulin secretion and beta cell loss, leading to elevated fasting blood glucose levels. A key complication of diabetes mellitus is diabetic retinopathy (DR), characterized by hyperglycemia-induced abnormalities in the retina. Adjacent to the retina lies the vitreous, a gelatinous matrix vital for ocular function. It harbors proteins and signaling molecules, offering insights into vitreous biology and ocular health. Moreover, as a reservoir for secreted molecules, the vitreous illuminates molecular processes within intraocular structures, especially under pathological conditions. To uncover the proteomic profile of porcine vitreous and explore its relevance to DR, we employed discovery proteomics to compare vitreous samples from INS^C94Y transgenic pigs and wild-type controls. Our analysis identified 1404 proteins, with 266 showing differential abundance in INS^C94Y vitreous. Notably, the abundances of ITGB1, COX2, and GRIFIN were significantly elevated in INS^C94Y vitreous. Gene Set Enrichment Analysis unveiled heightened MYC and mTORC1 signaling in INS^C94Y vitreous, shedding light on its biological significance in diabetes-associated ocular pathophysiology. These findings deepen our understanding of vitreous involvement in DR and provide valuable insights into potential therapeutic targets. Raw data are accessible via ProteomeXchange (PXD038198).