12,042 results match your criteria Proteomics[Journal]


Proteomics turns functional.

J Proteomics 2018 Dec 13. Epub 2018 Dec 13.

Department of Science and High Technology, Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy. Electronic address:

Proteomics is acquiring a pivotal role in the comprehensive understanding of human biology. Biochemical processes involved in complex diseases, such as neurodegenerative diseases, diabetes and cancer, can be identified by combining proteomics analysis and bioinformatics tools. In the last ten years, the main output of differential proteomics investigations evolved from long lists of proteins to the generation of new hypotheses and their functional verification. Read More

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December 2018

Response of the biomining Acidithiobacillus ferrooxidans to high cadmium concentrations.

J Proteomics 2018 Dec 13. Epub 2018 Dec 13.

Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile. Electronic address:

Cadmium is a heavy metal present in contaminated soils. It has no biological role but when entering cells generates DNA damage, overexpression of stress response proteins and misfolded proteins, amongst other deleterious effects. Acidithiobacillus ferrooxidans is an acidophilic bacterium resisting high concentrations of heavy metals such as cadmium. Read More

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December 2018

Corrigendum to "Comparative analysis of novel autoantibody isotypes against citrullinatedinter-alpha-trypsin inhibitor heavy chain 3 (ITIH3) 542-556 peptide in serum from Taiwanese females with rheumatoid arthritis, primary Sjögren's syndrome and secondary Sjögren's syndrome in rheumatoid arthritis" [J Proteomics 141: (2016) 1-11].

J Proteomics 2018 Dec 12. Epub 2018 Dec 12.

School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; PhD Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan. Electronic address:

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December 2018

Corrigendum to "Isotypes of autoantibodies against differentially expressed novel malondialdehyde-modifiedpeptide adducts in serum of Taiwanese women with rheumatoid arthritis" [J Proteomics 170: (2018) 141-150].

J Proteomics 2018 Dec 12. Epub 2018 Dec 12.

Department of Biotechnology and Animal Science, National Ilan University, Ilan 26047, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan. Electronic address:

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December 2018

A decade of Nucleic Acid Programmable Protein Arrays (NAPPA) availability: News, actors, progress, prospects and access.

J Proteomics 2018 Dec 12. Epub 2018 Dec 12.

Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain. Electronic address:

Understanding the dynamic of the proteome is a critical challenge because it requires high sensitive methodologies in high-throughput formats in order to decipher its modifications and complexity. While molecular biology provides relevant information about cell physiology that may be reflected in post-translational changes, High-Throughput (HT) experimental proteomic techniques are essential to provide valuable functional information of the proteins, peptides and the interconnections between them. Hence, many methodological developments and innovations have been reported during the last decade. Read More

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December 2018

Improved SILAC method for double labeling of bacterial proteome.

J Proteomics 2018 Dec 12. Epub 2018 Dec 12.

Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China. Electronic address:

Stable isotope labeling with amino acids in cell culture (SILAC) is a robust proteomics method with advantages such as reproducibility and easy handling. This method is popular for the analysis of mammalian cells. However, amino acid conversion in bacteria decreases the labeling efficiency and quantification accuracy, limiting the application of SILAC in bacterial proteomics to auxotrophic bacteria or to single labeling with lysine. Read More

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December 2018
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Early response of C2C12 myotubes to a sub-cytotoxic dose of hemorrhagic metalloproteinase HF3 from Bothrops jararaca venom.

J Proteomics 2018 Dec 12. Epub 2018 Dec 12.

Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil. Electronic address:

Manifestations of local tissue damage, such as hemorrhage and myonecrosis, are among the most dramatic effects of envenomation by viperid snakes. Snake venom metalloproteinases (SVMPs) of the P-III class are main players of the hemorrhagic effect due to their activities in promoting blood vessel disruption. Hemorrhagic Factor 3 (HF3), a P-III class SVMP from Bothrops jararaca, shows a minimum hemorrhagic dose of 240 fmol on rabbit skin. Read More

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December 2018
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Effects of hypoxia-reoxygenation stress on mitochondrial proteome and bioenergetics of the hypoxia-tolerant marine bivalve Crassostrea gigas.

J Proteomics 2018 Dec 11. Epub 2018 Dec 11.

Department of Marine Biology, University of Rostock, Rostock, Germany; Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany.

Mitochondria are key intracellular targets of hypoxia-reoxygenation (H/R) stress due to their central role in generation of ATP and reactive oxygen species (ROS). Intertidal oysters Crassostrea gigas are adapted to frequent H/R cycles and maintain aerobic function despite frequent oxygen fluctuations. To gain insight into the molecular mechanisms of H/R tolerance, we assessed changes in mitochondrial respiration and (phospho)proteome of C. Read More

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December 2018

Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish.

J Proteomics 2018 Dec 11. Epub 2018 Dec 11.

Laboratory of Evolutionary and Adaptive Physiology - Institute of Life, Earth and Environment - University of Namur, 61 Rue de Bruxelles, B5000 Namur, Belgium.

Early-life represents a critically sensitive window to endocrine disrupting chemicals, potentially leading to long-term repercussions on the phenotype later in life. The mechanisms underlying this phenomenon, referred to as the Developmental Origins of Health and Disease (DOHaD), are still poorly understood. To gain molecular understanding of these effects, we exposed mangrove rivulus (Kryptolebias marmoratus) for 28 days post hatching (dph) to 4 and 120 ng/L 17-α-ethinylestradiol, a model xenoestrogen. Read More

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December 2018

Development of a class prediction model to discriminate pancreatic ductal adenocarcinoma from pancreatic neuroendocrine tumor by MALDI mass spectrometry imaging.

Proteomics Clin Appl 2018 Dec 13:e1800046. Epub 2018 Dec 13.

R. Casadonte, J. Kriegsmann, Proteopath GmbH, Trier, Germany.

Purpose: To define proteomic differences between pancreatic ductal adenocarcinoma (pDAC) and pancreatic neuroendocrine tumor (pNET) by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI).

Experimental Design: 93 pDAC and 126 pNET individual tissues were assembled in tissue microarrays and analyzed by MALDI MSI. The cohort was separated in a training (52 pDAC and 83 pNET) and validation set (41 pDAC and 43 pNET). Read More

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December 2018

Immunoproteomic Identification of Non-carbohydrate Antigens Eliciting Graft-Specific Adaptive Immune Responses in Patients with Bovine Pericardial Bioprosthetic Heart Valves.

Proteomics Clin Appl 2018 Dec 13:e1800129. Epub 2018 Dec 13.

Dr. K. V. Gates, Dr. Q. Xing, Dr. L. G. Griffiths, Department of Cardiovascular Diseases, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

Purpose: The purpose of this case-control retrospective discovery study is to identify antigenic bovine pericardium (BP) proteins that stimulate graft-specific humoral immune response in patients implanted with glutaraldehyde fixed bovine pericardial (GFBP) heart valves.

Experimental Design: Banked serum was collected from age and sex matched patients who had received either a GFBP or mechanical heart valve replacement. Serum IgG was isolated and used to generate poly-polyclonal antibody affinity chromatography columns from each patient. Read More

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December 2018

Can Mass Spectrometry Imaging become an Integral Part of a Pathologist's Toolkit?

Authors:
Erin H Seeley

Proteomics Clin Appl 2018 Dec 13:e1800180. Epub 2018 Dec 13.

E. H. Seeley, New River Labs, LLC, Morgantown, WV, USA.

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December 2018

Proteomic Evidence of Biological Ageing in a Child with a Compound Heterozygous ZMPSTE24 Mutation.

Proteomics Clin Appl 2018 Dec 13:e1800135. Epub 2018 Dec 13.

A. K. Lucas-Herald, B. Mansoorian, W. Mullen, C. Delles, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK.

Background: Progeria-like syndromes offer a unique insight into ageing. Here we present the case of a boy affected with mandibuloacral dysplasia and compound heterozygous mutations in ZMPSTE24.

Methods: Capillary electrophoresis-mass spectroscopy was used for proteome analysis to analyse peptides previously found to be differentially regulated in chronic kidney disease (273 peptides defining the CKD273 classifier), coronary artery disease (238 peptides defining the CAD238 classifier) and ageing (116 peptides defining the AGE116 classifier). Read More

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December 2018

figHigh Spatial Resolution MALDI-MS Imaging in the Study of Membranous Nephropathy.

Proteomics Clin Appl 2018 Dec 7:e1800016. Epub 2018 Dec 7.

University of Milano-Bicocca, Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy.

MALDI-MSI technology has advanced rapidly during recent years with the development of instruments equipped with low-diameter lasers that are suitable for high spatial resolution imaging. This may provide significant advantages in certain fields of molecular pathology where more specific protein fingerprints of individual cell types are required, such as renal pathology. Here we performed MALDI-MSI analysis of a cohort of MN patients among which patients either responded favourably (R; n = 6), or unfavourably (NR; n = 4), to immunosuppressive treatment (Ponticelli Regimen), employing a 10μm laser spot diameter. Read More

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December 2018

Proteomic Analysis of the initial Oral Pellicle in Caries-Active and Caries-Free Individuals.

Proteomics Clin Appl 2018 Dec 8:e1800143. Epub 2018 Dec 8.

Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, University Hospital, Saarland University, Homburg/Saar, Germany.

Purpose: To 1) elucidate individual proteomic profiles of the 3-min biofilm of caries-active and caries-free individuals and 2) compare these proteomic profiles against the background of caries.

Experimental Design: The initial oral pellicle of 12 caries-active and 12 caries-free individuals was generated in situ on ceramics specimens. The individual, host-specific proteomic profiles of this basic pellicle layer were analyzed by a chemical elution protocol combined with an elaborate mass spectrometry and evaluated bioinformatically. Read More

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December 2018

Identification of MALDI Imaging Proteolytic Peptides using LC-MS/MS-Based Biomarker Discovery Data - A Proof of Concept.

Proteomics Clin Appl 2018 Dec 7:e1800158. Epub 2018 Dec 7.

Institute of Pathology, University of Heidelberg, Heidelberg, Germany.

Purpose: Identification of proteolytic peptides from matrix-assisted laser desorption/ionization (MALDI) imaging still remains a challenge. In-situ post source decay leads to low fragmentation yields, so identification is often impaired. Liquid chromatography tandem mass spectrometry (LC-MS/MS) is an alternative to in-situ MS/MS, but leads to multiple identification candidates for a given mass. Read More

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December 2018

Proteomic insights into lysine acetylation and the implications for medical research.

Expert Rev Proteomics 2018 Dec 7. Epub 2018 Dec 7.

a Laboratorio de Proteómica, Centro de Ciencias Genómicas , Universidad Nacional Autónoma de México , Cuernavaca , Morelos C. P. 62210, México .

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December 2018

Towards the molecular deciphering of Pomacea canaliculata immunity: first proteomic analysis of circulating hemocytes.

Proteomics 2018 Dec 10:e1800314. Epub 2018 Dec 10.

Department of Life Sciences, 41125, Modena, Italy.

Pomacea canaliculata is a freshwater snail with interesting biological features that include invasiveness, human parasite hosting and adult regeneration. Its immune system may represent the target for strategies aimed at controlling the spread of the snail population and its hosting of the human parasite Angiostrongylus cantonensis. Moreover, immune functions likely have a role in the snail's ability to wound heal and regenerate. Read More

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December 2018
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Scavager: a versatile postsearch validation algorithm for shotgun proteomics based on gradient boosting.

Proteomics 2018 Dec 8:e1800280. Epub 2018 Dec 8.

Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia.

Shotgun proteomics workflows for database protein identification typically include a combination of search engines and postsearch validation software based mostly on machine learning algorithms. Here we present a new postsearch validation tool called Scavager employing CatBoost, an open-source gradient boosting library, which shows improved efficiency compared with the other popular algorithms, such as Percolator, PeptideProphet, and Q-ranker. The comparison was done using multiple data sets and search engines, including MSGF+, MSFragger, X!Tandem, Comet, and recently introduced IdentiPy. Read More

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December 2018

Quantitative Proteomics by SWATH-MS Suggest an Association Between Circulating Exosomes and Maternal Metabolic Changes in Gestational Diabetes Mellitus.

Proteomics 2018 Dec 7:e1800164. Epub 2018 Dec 7.

Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, QLD, 4029, Australia.

Several factors including placental hormones (PH) released from the human placenta have been associated with the development of insulin resistance and gestational diabetes mellitus (GDM). However, circulating levels of PH do not correlate well with maternal insulin sensitivity across gestation, suggesting that other, previously unrecognized, mechanisms may be involved. The levels of circulating exosomes are higher in GDM compared to normal. Read More

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December 2018
3.807 Impact Factor

A Combination of Proteomic Approaches Identifies A Panel of Circulating Extracellular Vesicle Proteins Related to the Risk of Suffering Cardiovascular Disease in Obese Patients.

Proteomics 2018 Dec 7:e1800248. Epub 2018 Dec 7.

Platelet Proteomics Group. Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.

Plasma-derived extracellular vesicles (EVs) have been extensively described as putative biomarkers in different diseases. Interestingly, increased levels of EVs subpopulations are well-known to associate with obesity. The goal of this study was to identify EVs-derived biomarkers in plasma from obese patients in order to predict the development of pathological events associated with obesity. Read More

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December 2018
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Ecotoxicoproteomics: A decade of progress in our understanding of anthropogenic impact on the environment.

J Proteomics 2018 Dec 6. Epub 2018 Dec 6.

Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France. Electronic address:

Anthropogenic pollutants are found worldwide. Their fate and effects on human and ecosystem health must be appropriately monitored. Today, ecotoxicology is focused on the development of new methods to assess the impact of pollutant toxicity on living organisms and ecosystems. Read More

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December 2018
3 Reads

A proteomic approach to identify novel disease biomarkers in LCAT deficiency.

J Proteomics 2018 Dec 6. Epub 2018 Dec 6.

Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy. Electronic address:

Genetic LCAT deficiency is a rare recessive autosomal disease due to loss-of-function mutations in the gene coding for the enzyme lecithin:cholesterol acyltransferase (LCAT). Homozygous carriers are characterized by corneal opacity, haemolytic anaemia and renal disease, which represent the first cause of morbidity and mortality in these subjects. Diagnostic and prognostic markers capable of early detecting declining kidney function in these subjects are not available, and the specific serum or urine proteomic signature of LCAT deficient carriers has never been assessed. Read More

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December 2018

Statistical analysis of proteomics data: A review on feature selection.

J Proteomics 2018 Dec 6. Epub 2018 Dec 6.

Department of Science and High Technology (DiSAT), University of Insubria, Busto Arsizio, Italy. Electronic address:

The spread of "-omics" strategies has strongly changed the way of thinking about the scientific method. Indeed, managing huge amounts of data imposes the replacement of the classical deductive approach with a data-driven inductive approach, so to generate mechanistical hypotheses from data. Data reduction is a crucial step in the process of proteomics data analysis, because of the sparsity of significant features in big datasets. Read More

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December 2018

Postmortem protein stability investigations of the human hepatic drug-metabolizing cytochrome P450 enzymes CYP1A2 and CYP3A4 using mass spectrometry.

J Proteomics 2018 Dec 7. Epub 2018 Dec 7.

Department of Forensic Medicine, Aarhus University, Denmark.

Variability in expression and activity of hepatic drug-metabolizing cytochrome P450 (CYP) enzymes can play a causal role in fatal intoxication cases and is thus of forensic interest. We investigated the feasibility of LC-MS/MS based quantification and in vitro enzyme activity measurements of two major drug-metabolizing enzymes CYP1A2 and CYP3A4 in postmortem human liver microsomes (HLM). In autopsy cases (postmortem interval 24-36 h) we found CYP1A2 and CYP3A4 protein levels similar to that measured in a non-decayed reference HLM pool, whereas CYP1A2 and CYP3A4 enzyme activities were absent or severely decreased. Read More

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December 2018

Proteomic analysis of protein homeostasis and aggregation.

J Proteomics 2018 Dec 6. Epub 2018 Dec 6.

Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80308, Poland. Electronic address:

Protein homeostasis (proteostasis) refers to the ability of cells to preserve the correct balance between protein synthesis, folding and degradation. Proteostasis is essential for optimal cell growth and survival under stressful conditions. Various extracellular and intracellular stresses including heat shock, oxidative stress, proteasome malfunction, mutations and aging-related modifications can result in disturbed proteostasis manifested by enhanced misfolding and aggregation of proteins. Read More

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December 2018

Quantifying proteins at microgram levels integrating gel electrophoresis and smartphone technology.

J Proteomics 2018 Dec 7. Epub 2018 Dec 7.

Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Brazil. Electronic address:

A combination between gel electrophoresis and smartphone technology is applied for quantifying proteins in a serum sample. Electrophoresis not only allows one to separate different proteins but also to build-up a calibration curve for those proteins. To expand its applicability, a smartphone allows one to capture a gel image, through its camera. Read More

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December 2018

Proteomic analysis of olfactory bulb suggests CACNA1E as a promoter of CREB signaling in microbiota-induced depression.

J Proteomics 2018 Dec 4. Epub 2018 Dec 4.

Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing 400016, China; Department of Neurology, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China. Electronic address:

Major depressive disorders impact approximately 17% of the population worldwide, whose high morbidity and considerable adversity have resulted in enormous social and economic burden. In addition, clinically depressed patients often show reduced volume of olfactory bulb (OB) and decreased olfactory sensitivity. Although mounting evidence conveyed that the gut microbiota may implicate the pathophysiology of major depressive disorder (MDD) via the microbe-gut-brain axis, knowledge about its distinctive molecular mechanism is rudimentary. Read More

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December 2018
3 Reads

Dirhodium (II) complex interferes with iron-transport system to exert antibacterial action against Streptococcus pneumoniae.

J Proteomics 2018 Dec 4. Epub 2018 Dec 4.

Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China. Electronic address:

Drug resistance in bacteria is becoming a significant threat to global public health, and the development of novel and efficient antibacterial compounds is urgently needed. Recently, rhodium complexes have attracted attention as antimicrobial agents, yet their antibacterial mechanism remains unknown. In this study, we observed that the dirhodium (II) complex RhAc inhibited Streptococcus. Read More

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December 2018
2 Reads

An integrated quantitative proteomic and metabolomics approach to reveal the negative regulation mechanism of LamB in antibiotics resistance.

J Proteomics 2018 Dec 4. Epub 2018 Dec 4.

Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences), Fujian Agriculture and Forestry University, Fuzhou 350002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, PR China. Electronic address:

Previously, a maltose-specific channel porin, LamB was found to be associate with multi-drug resistance in a lamB deleted strain, but the exact mechanisms require further elucidation. Herein, differential protein expression between the Escherichia coli mutant strain ΔlamB and the wild type strain BW25113, with and without ciprofloxacin (CFLX), was identified using iTRAQ based liquid chromatography-tandem mass spectrometry (LC-MS/MS); while differential metabolite expression was examined using gas chromatography-mass spectrometry (GC-MS). Further Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that lamB deletion leads to a decrease in several key metabolic pathways such as tricarboxylic acid (TCA) cycle, pentose phosphate pathway and glycolysis/gluconeogenesis. Read More

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December 2018
3 Reads

PPICurator: a tool for extracting comprehensive protein-protein interaction information.

Proteomics 2018 Dec 6:e1800291. Epub 2018 Dec 6.

State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, 102206, P. R. China.

PPI extraction through biological literature curation has been widely employed for proteome analysis. There is a strong need for a tool that can assist researchers in extracting comprehensive PPI information through literature curation, which is critical in research on protein, e.g. Read More

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December 2018
7 Reads

Proteins regulating microvesicle biogenesis and multidrug resistance in cancer.

Authors:
J Taylor M Bebawy

Proteomics 2018 Dec 6:e1800165. Epub 2018 Dec 6.

Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney, Sydney, Australia.

Microvesicles (MV) are emerging as important mediators of intercellular communication. These signalling vectors are implicated in physiological processes ranging from vascular homeostasis to inflammation. They also play an important role in the cancer pathology and progression. Read More

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December 2018
2 Reads

Cytomine: towards an open and collaborative software platform for digital pathology bridged to molecular investigations.

Proteomics Clin Appl 2018 Dec 6:e1800057. Epub 2018 Dec 6.

Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium.

Purpose: Digital histology is being increasingly used in research and clinical applications. In parallel new tissue imaging methods (e.g. Read More

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December 2018
3 Reads

Implementation of clinical proteomics: A step closer to personalised medicine?

Authors:
Antonia Vlahou

Proteomics Clin Appl 2018 Dec 6:e1800088. Epub 2018 Dec 6.

Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527, Athens, Greece.

The success of clinical proteomics, per definition, is ultimately defined by the clinical implementation of proteomics findings. Extensive research activity in the field, targeting especially biomarker discovery, has been conducted the past decades, with several studies suggesting a benefit from proteome based application in patient management. This viewpoint article discusses the current status in clinical proteomics with respect to implementation, (as evidenced by use of protein findings in drug labeling and patient stratification), and proposes specific action points for accelerating the biomarker validation process, placing special emphasis on the importance of data and resource sharing. Read More

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December 2018

Proteomic Landscape of Cholangiocarcinomas Reveals 3 Different Subgroups According to their Localization and the Aspect of Non-Tumor Liver.

Proteomics Clin Appl 2018 Dec 6:e1800128. Epub 2018 Dec 6.

UMR 1149 INSERM - Paris Diderot University, Inflammation Research Center, Paris, France.

Purpose: Cholangiocarcinomas (CC), tumors derived from epithelial biliary cells, define a heterogeneous entity based upon their anatomic localization (intra- versus extrahepatic) and, for those developing in the liver, depending on the aspect of non-tumor liver (normal versus cirrhosis). The aim of the study was to characterize the molecular heterogeneity of the different types of CC by a global proteomic approach.

Experimental Design: Thirty-three tumor samples from 17 intrahepatic CC (iCC) including 9 and 8 developed on normal (iCC ) and cirrhotic liver (iCC ), respectively; 5 hilar CC (CC ), 5 CC developed in the pancreatic portion of the bile duct (CC ) and 6 hepatocellular carcinoma (HCC), were submitted to label-free quantitative proteomic analysis. Read More

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December 2018
1 Read
2.683 Impact Factor

Functional study of Carboxylesterase 1 protein isoforms.

Proteomics 2018 Dec 5:e1800288. Epub 2018 Dec 5.

Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan, US.

Carboxylesterase1 (CES1) is a primary human hepatic hydrolase involved in hydrolytic biotransformation of numerous medications. Considerable interindividual variability in CES1 expression and activity has been consistently reported. Four isoforms of the CES1 protein are produced by alternative splicing (AS). Read More

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December 2018
4 Reads

Proteomics Analysis of Thermoplasma Quinone Droplets.

Proteomics 2018 Dec 5:e1800317. Epub 2018 Dec 5.

Department of Applied and Environmental Microbiology, National Agricultural Research and Innovation Centre, H-1022, Budapest, Hungary.

A novel type of lipid droplet/lipoprotein (LD/LP) particle from Thermoplasma acidophilum has been identified recently, and based on biochemical evidences it was named Thermoplasma Quinone Droplet (TaQD). The major components of TaQDs are menaquinones, and to some extent polar lipids, and the 153 amino acid long Ta0547 vitellogenin-N domain protein. In this paper we aimed to identify TaQD proteome components with 1D-SDS-PAGE/Lc-MS/MS and cross reference them with Edman degradation. Read More

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December 2018
2 Reads

Targeted Feature Extraction in MALDI Mass Spectrometry Imaging to Discriminate Proteomic Profiles of Breast and Ovarian Cancer.

Proteomics Clin Appl 2018 Dec 6:e1700168. Epub 2018 Dec 6.

University of Bremen, Bremen, Germany.

Purpose: To develop a mass spectrometry imaging (MSI) based workflow for extracting m/z values related to putative protein biomarkers and using these for reliable tumor classification.

Experimental Design: Given a list of putative breast and ovarian cancer biomarker proteins, we extracted a set of related m/z values from heterogeneous MSI datasets derived from formalin-fixed paraffin-embedded tissue material. Based on these features, a linear discriminant analysis classification model was trained to discriminate the two tumor types. Read More

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December 2018
1 Read

Identification of Saliva Proteins of Spider Mite Tetranychus evansi by Transcriptome and LC-MS/MS Analyses.

Proteomics 2018 Dec 5:e1800302. Epub 2018 Dec 5.

Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.

The spider mite Tetranychus evansi has a remarkable ability to suppress and manipulate plant defenses, which makes it an ideal model to investigate plant-herbivores interactions. In this study, we performed a de novo assembly of the transcriptome of T. evansi, and characterized the proteins in its secreted saliva by Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). Read More

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December 2018
3 Reads

Characterizations of HSP90-interacting complex in renal cells using tandem affinity purification and its potential role in kidney stone formation.

Proteomics 2018 Dec 3:e1800004. Epub 2018 Dec 3.

Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.

Heat shock protein 90 (HSP90) is a highly abundant molecular chaperone that interacts with many other intracellular proteins to regulate various cellular processes. However, compositions of the HSP90-interacting complex remain underinvestigated. This study thus aimed to characterize such complex in human embryonic kidney (HEK293T) cells under normal physiologic state using tandem affinity purification (TAP) followed by protein identification using an ultrahigh-resolution tandem mass spectrometer (Qq-TOF MS/MS). Read More

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December 2018
1 Read

Oncolytic adenovirus Delta-24-RGD induces a widespread glioma proteotype remodeling during autophagy.

J Proteomics 2018 Nov 29. Epub 2018 Nov 29.

Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain; IDISNA, Navarra Institute for Health Research, Pamplona, Spain; Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain. Electronic address:

Adenovirus Delta-24-RGD has shown a remarkable efficacy in a phase I clinical trial for glioblastoma. Delta-24-RGD induces autophagy in glioma cells, however, the molecular derangements associated with Delta-24-RGD infection remains poorly understood. Here, proteomics was applied to characterize the glioma metabolic disturbances soon after Delta-24-RGD internalization and late in infection. Read More

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November 2018
1 Read

Trypanosoma cruzi immunoproteome: Calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy.

J Proteomics 2018 Nov 29. Epub 2018 Nov 29.

Laboratório de Biologia Celular, IOC, Fiocruz, Rio de Janeiro, RJ, Brazil. Electronic address:

Chagas disease, caused by the protozoan Trypanosoma cruzi, affects millions of people worldwide, especially in Latin America. Approximately 30% of the cases evolve to the chronic symptomatic stage due to cardiac and/or digestive damage, generally accompanied by nervous system impairment. Given the higher frequency and severity of clinical manifestations related to cardiac tissue lesion, the goal of this study was the identification of proteins associated with the disease progression towards its cardiac form. Read More

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November 2018
1 Read

Comparative proteomics of Tobacco mosaic virus-infected Nicotiana tabacum plants identified major host proteins involved in photosystems and plant defence.

J Proteomics 2018 Nov 29. Epub 2018 Nov 29.

Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, 117543, Singapore; Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu 215123, China. Electronic address:

Tobacco mosaic virus (TMV) is a positive single-stranded RNA virus. Its 5' end ORF codes for the replicase proteins, namely 126 kDa and 183 kDa, respectively. These proteins interact with many host proteins to form a virus replication complex (VRC). Read More

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November 2018
1 Read
3.888 Impact Factor

Standard abbreviations.

Authors:

Proteomics 2018 Dec;18(23):e1870204

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December 2018

Proteomics of Uterosacral Ligament Connective Tissue from Women With and Without Pelvic Organ Prolapse.

Proteomics Clin Appl 2018 Dec 5:e1800086. Epub 2018 Dec 5.

The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China.

Purpose: Damage to the uterosacral ligaments is an important contributor to uterine and vaginal prolapse. The aim of this study was to identify differentially expressed proteins in the uterosacral ligaments of women with and without pelvic organ prolapse and analyze their relationships to cellular mechanisms involved in the pathogenesis of pelvic organ prolapse.

Experimental Design: Uterosacral ligament connective tissue from four patients with pelvic organ prolapse and four control women underwent iTRAQ analysis followed by Ingenuity Pathway Analysis of differentially expressed proteins. Read More

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December 2018
1 Read

In vitro and in vivo Proteomic Comparison of Human Neural Progenitor Cell-Induced Photoreceptor Survival.

Proteomics 2018 Dec 4:e1800213. Epub 2018 Dec 4.

Department of Biomedical Sciences, Cedars-Sinai Medical Center.

Retinal degenerative diseases are some of the leading causes of blindness with few treatments. Various cell-based therapies have aimed to slow the progression of vision loss by preserving light-sensing photoreceptor cells. A subretinal injection of human neural progenitor cells (hNPCs) into the Royal College of Surgeons (RCS) rat model of retinal degeneration has aided in photoreceptor survival, though the mechanisms are mainly unknown. Read More

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December 2018
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A Double-Edged Sword:Complement Component 3 in Toxoplasma gondii Infection.

Proteomics 2018 Dec 4:e1800271. Epub 2018 Dec 4.

College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, P. R. China.

We artificially infected Sprague Dawley (SD) rats and Kunming (KM) mice with type II Toxoplasma gondii (T. gondii) strain Prugniaud (Pru) to generate toxoplasmosis, which is a fatal disease mediated by T. gondii invasion of the central nervous system (CNS) by unknown mechanisms. Read More

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December 2018
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Contribution of Plasmodium immunomics: potential impact for serological testing and surveillance of malaria.

Expert Rev Proteomics 2018 Dec 4. Epub 2018 Dec 4.

a Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health , National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases , Shanghai 200025 , People's Republic of China.

Introduction: Plasmodium vivax and P. knowlesi account together for a considerable share of the global burden of malaria, along with P. falciparum. Read More

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December 2018
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2.896 Impact Factor

In-Cell NMR Spectroscopy of Intrinsically Disordered Proteins.

Proteomics 2018 Nov 29:e1800055. Epub 2018 Nov 29.

Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA.

This review summarizes the results of in-cell NMR spectroscopic investigations of the eukaryotic and prokaryotic IDPs: α-synuclein, prokaryotic ubiquitin-like protein, Pup, tubulin-related neuronal protein, Tau, phenylalanyl-glycyl-repeat-rich nucleoporins, FG Nups, and the negative regulator of flagellin synthesis, FlgM. The results show that the cellular behavior of IDPs may differ significantly from that observed in the test tube. This article is protected by copyright. Read More

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November 2018
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Integrated Eutopic Endometrium and Non-Depleted Serum Quantitative Proteomic Analysis Identifies Candidate Serological Markers of Endometriosis.

Proteomics Clin Appl 2018 Nov 28:e1800153. Epub 2018 Nov 28.

Human Development and Health, University of Southampton, Southampton, SO16, UK.

Background: Endometriosis affects about 4% of women in the reproductive age and is associated with subfertility. The aim of the present study is to examine the integrated quantitative proteomic profile of eutopic endometrium and serum from women with endometriosis compared to controls in order to identify candidate disease-specific serological markers.

Methods: Eutopic endometrium and serum from patients with endometriosis (n = 8 for tissue and n = 4 for serum) are, respectively, compared to endometrium and serum from females without endometriosis (n = 8 for tissue and n = 4 for serum) using a shotgun quantitative proteomics method. Read More

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November 2018
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2.680 Impact Factor