Proteomics最新文献

Plasma proteomics offers high potential for biomarker discovery, as plasma is collected through a minimally invasive procedure and constitutes the most complex human-derived proteome. However, the wide dynamic range poses a significant challenge. Here, we propose a semi-automated method based on the use of multiple single chain variable fragment antibodies, each enriching for peptides found in up to a few hundred proteins. This approach allows for the analysis of a complementary fraction compared to full proteome analysis. Proteins from pooled plasma were extracted and digested before testing the performance of 29 different antibodies with the aim of reproducibly maximizing peptide enrichment. Our results demonstrate the enrichment of 3662 peptides not detected in neat plasma or negative controls. Moreover, most antibodies were able to enrich for at least 155 peptides across different levels of abundance in plasma. To further reduce analysis time, a combination of antibodies was used in a multiplexed setting. Repeated sample analyses showed low coefficients of variation, and the method is flexible in terms of affinity binders. It does not impose drastic increases in instrument time, thus showing excellent potential for usage in large scale discovery projects.

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.

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.

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.