Proteomes, Vol. 12, Pages 13: Key Proteomics Tools for Fundamental and Applied Microalgal Research Proteomes doi: 10.3390/proteomes12020013 Authors: Maxence Plouviez Eric Dubreucq Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technologic ..read more

Proteomes, Vol. 12, Pages 12: Comprehensive Proteome Profiling of a Xanthomonas campestris pv. Campestris B100 Culture Grown in Minimal Medium with a Specific Focus on Nutrient Consumption and Xanthan Biosynthesis Proteomes doi: 10.3390/proteomes12020012 Authors: Ben Struck Sanne Jitske Wiersma Vera Ortseifen Alfred Pühler Karsten Niehaus Xanthan, a bacterial polysaccharide, is widespread in industrial applications, particularly as a food additive. However, little is known about the process of xanthan synthesis on the proteome level, even though Xanthomonas campestris is frequently used for xa ..read more

Proteomes, Vol. 12, Pages 11: Integration of Urinary Peptidome and Fecal Microbiome to Explore Patient Clustering in Chronic Kidney Disease Proteomes doi: 10.3390/proteomes12020011 Authors: Mavrogeorgis Valkenburg Siwy Latosinska Glorieux Mischak Jankowski Millions of people worldwide currently suffer from chronic kidney disease (CKD), requiring kidney replacement therapy at the end stage. Endeavors to better understand CKD pathophysiology from an omics perspective have revealed major molecular players in several sample sources. Focusing on non-invasive sources, gut microbial communities appea ..read more

Proteomes, Vol. 12, Pages 10: Cadmium Highlights Common and Specific Responses of Two Freshwater Sentinel Species, Dreissena polymorpha and Dreissena rostriformis bugensis Proteomes doi: 10.3390/proteomes12020010 Authors: Florence Bultelle Aimie Le Saux Elise David Arnaud Tanguy Simon Devin Stéphanie Olivier Agnès Poret Philippe Chan Fanny Louis Laurence Delahaut Sandrine Pain-Devin Romain Péden David Vaudry Frank Le Foll Béatrice Rocher Zebra mussel (ZM), Dreissena polymorpha, commonly used as a sentinel species in freshwater biomonitoring, is now in competition for habitat with quagga mussel ..read more

Proteomes, Vol. 12, Pages 8: Biomarkers in Ovarian Cancer: Towards Personalized Medicine Proteomes doi: 10.3390/proteomes12010008 Authors: López-Portugués Montes-Bayón Díez Ovarian cancer is one of the deadliest cancers in women. The lack of specific symptoms, especially at the initial stages of disease development, together with the malignancy heterogeneity, lower the life expectancy of patients. Aiming to improve survival rates, diagnostic and prognostic biomarkers are increasingly employed in clinics, providing gynecologists and oncologists with new tools to guide their treatment decisions ..read more

Proteomes, Vol. 12, Pages 7: Quantitative Proteomics Reveal Region-Specific Alterations in Neuroserpin-Deficient Mouse Brain and Retina: Insights into Serpini1 Function Proteomes doi: 10.3390/proteomes12010007 Authors: Shahab Mirshahvaladi Nitin Chitranshi Ardeshir Amirkhani Rashi Rajput Devaraj Basavarajappa Roshana Vander Wall Dana Pascovici Angela Godinez Giovanna Galliciotti Joao A. Paulo Veer Gupta Stuart L. Graham Vivek Gupta Mehdi Mirzaei Neural regeneration and neuroprotection represent strategies for future management of neurodegenerative disorders such as Alzheimer’s di ..read more

Proteomes, Vol. 12, Pages 6: Observations from the Proteomics Bench Proteomes doi: 10.3390/proteomes12010006 Authors: Simone König Karin Schork Martin Eisenacher Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrom ..read more

Proteomes, Vol. 12, Pages 5: Enhanced Electrophoretic Depletion of Sodium Dodecyl Sulfate with Methanol for Membrane Proteome Analysis by Mass Spectrometry Proteomes doi: 10.3390/proteomes12010005 Authors: Hammam H. Said Alan A. Doucette Membrane proteins are underrepresented during proteome characterizations, primarily owing to their lower solubility. Sodium dodecyl sulfate (SDS) is favored to enhance protein solubility but interferes with downstream analysis by mass spectrometry. Here, we present an improved workflow for SDS depletion using transmembrane electrophoresis (TME) while retaining ..read more

Proteomes, Vol. 12, Pages 4: How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes doi: 10.3390/proteomes12010004 Authors: Paul Dowling Capucine Trollet Elisa Negroni Dieter Swandulla Kay Ohlendieck This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogeneti ..read more

Proteomes, Vol. 12, Pages 3: The Mechanisms of Regulated Cell Death: Structural and Functional Proteomic Pathways Induced or Inhibited by a Specific Protein—A Narrative Review Proteomes doi: 10.3390/proteomes12010003 Authors: Diego Fernández-Lázaro Begoña Sanz Jesús Seco-Calvo Billions of cells die in us every hour, and our tissues do not shrink because there is a natural regulation where Cell Death (CD) is balanced with cell division. The process in which cells eliminate themselves in a controlled manner is called Programmed Cell Death (PCD). The PCD plays an important role during e ..read more