73,568 results match your criteria proteins proteomics

Ultrafiltration strategy combined with nanoLC-MS/MS based proteomics for monitoring potential residual proteins in TCMIs.

J Chromatogr B Analyt Technol Biomed Life Sci 2021 May 30;1178:122818. Epub 2021 May 30.

Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China. Electronic address:

Traditional Chinese medicine injections (TCMIs) containing complex constituents frequently cause unpredictable adverse reactions. The residual heterologous proteins in TCMIs may be one kind of the sensitized constituents. However, few methods were developed to identify and monitor the residual proteins of TCMIs in industry. Read More

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Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs.

Mol Cell Proteomics 2021 Jun 12:100109. Epub 2021 Jun 12.

Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Many small open reading frames (smORFs) embedded in lncRNA transcripts have been shown to encode biologically functional polypeptides (smORFs-encoded polypeptides, SEPs) in different organisms. Despite significant advances in genomics, bioinformatics and proteomics that largely enabled the discovery of novel SEPs, their identification across different biological samples is still hampered by their poor predictability, diminutive size and low relative abundance. Here, we take advantage of NONCODE, a repository containing the most complete collection and annotation of lncRNA transcripts from different species, to build a novel database that attempts to maximize a collection of SEPs from human and mouse lncRNA transcripts. Read More

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Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer.

Mol Cell Proteomics 2021 Jun 12:100115. Epub 2021 Jun 12.

Department of Gastrointestinal Surgery, National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China. Electronic address:

The occurrence and prevalence of colorectal cancer (CRC) is closely associated with age. More than 90% of CRC patients are diagnosed after 50 years old. However, CRC incidence of young individuals has been increasing since 1990s as overall CRC frequency declining. Read More

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Multi-cohort profiling reveals elevated CSF levels of brain-enriched proteins in Alzheimer's disease.

Ann Clin Transl Neurol 2021 Jun 15. Epub 2021 Jun 15.

Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.

Objective: Decreased amyloid beta (Aβ) 42 together with increased tau and phospho-tau in cerebrospinal fluid (CSF) is indicative of Alzheimer's disease (AD). However, the molecular pathophysiology underlying the slowly progressive cognitive decline observed in AD is not fully understood and it is not known what other CSF biomarkers may be altered in early disease stages.

Methods: We utilized an antibody-based suspension bead array to analyze levels of 216 proteins in CSF from AD patients, patients with mild cognitive impairment (MCI), and controls from two independent cohorts collected within the AETIONOMY consortium. Read More

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The Serum Proteome and Ursodeoxycholic Acid Response in Primary Biliary Cholangitis.

Hepatology 2021 Jun 15. Epub 2021 Jun 15.

Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK.

Background And Aims: Stratified therapy has entered clinical practice in primary biliary cholangitis (PBC), with routine use of second-line therapy in non-responders to first-line therapy with ursodeoxycholic acid (UDCA). The mechanism for non-response to UDCA remains, however, unclear and we lack mechanistic serum markers. The UK-PBC study was established to explore the biological basis of UDCA non-response in PBC and to identify markers to enhance treatment. Read More

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Quantitative Temporal Viromics.

Annu Rev Virol 2021 Jun 15. Epub 2021 Jun 15.

Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom; email:

The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry-based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. Read More

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Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs.

J Cell Biol 2021 Jul 15;220(7). Epub 2021 Jun 15.

Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

Rab11 GTPase proteins are required for cytokinesis, ciliogenesis, and lumenogenesis. Rab11a is critical for apical delivery of podocalyxin (PODXL) during lumen formation in epithelial cells. SH3BP5 and SH3BP5L are guanine nucleotide exchange factors (GEFs) for Rab11. Read More

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Antibody Levels to Plasmodium falciparum Erythrocyte Membrane Protein 1-DBLγ11 and DBLδ-1 Predict Reduction in Parasite Density.

mSystems 2021 Jun 15:e0034721. Epub 2021 Jun 15.

Molecular and Pathogenesis Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology (LMIV), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, USA.

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a variant surface antigen family expressed on infected red blood cells that plays a role in immune evasion and mediates adhesion to vascular endothelium. PfEMP1s are potential targets of protective antibodies as suggested by previous seroepidemiology studies. Here, we used previously reported proteomic analyses of PfEMP1s of clinical parasite isolates collected from Malian children to identify targets of immunity. Read More

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Recent advances (2019-2021) of capillary electrophoresis-mass spectrometry for multilevel proteomics.

Mass Spectrom Rev 2021 Jun 15. Epub 2021 Jun 15.

Department of Chemistry, Michigan State University, East Lansing, Michigan, USA.

Multilevel proteomics aims to delineate proteins at the peptide (bottom-up proteomics), proteoform (top-down proteomics), and protein complex (native proteomics) levels. Capillary electrophoresis-mass spectrometry (CE-MS) can achieve highly efficient separation and highly sensitive detection of complex mixtures of peptides, proteoforms, and even protein complexes because of its substantial technical progress. CE-MS has become a valuable alternative to the routinely used liquid chromatography-mass spectrometry for multilevel proteomics. Read More

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Plasma Proteomics of COVID-19 Associated Cardiovascular Complications: Implications for Pathophysiology and Therapeutics.

Res Sq 2021 Jun 8. Epub 2021 Jun 8.

Cardiovascular complications are common in COVID-19 and strongly associated with disease severity and mortality. However, the mechanisms driving cardiac injury and failure in COVID-19 are largely unknown. We performed plasma proteomics on 80 COVID-19 patients and controls, grouped according to disease severity and cardiac involvement. Read More

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Liver Proteome Profile of Growth Restricted and Appropriately Grown Newborn Wistar Rats Associated With Maternal Undernutrition.

Front Endocrinol (Lausanne) 2021 28;12:684220. Epub 2021 May 28.

Second Department of Obstetrics and Gynaecology, Medical School, National and Kapodistrian University of Athens, Athens, Greece.

Background: Fetal growth restriction (FGR) has been associated with adverse perinatal outcomes and epigenetic modifications that impact gene expression leading to permanent changes of fetal metabolic pathways and thereby influence development of disease in childhood and adult life. In this study, we investigated the result of maternal food restriction on liver protein expression in Wistar male newborn pups.

Materials & Methods: Ten (n = 10) timed pregnant Wistar rats on their 14th day of gestation were randomly assigned to either control (n = 4) or food restricted group (n = 6). Read More

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Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells.

Oncogene 2021 Jun 14. Epub 2021 Jun 14.

Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.

Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. Read More

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Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics.

Sci Rep 2021 Jun 14;11(1):12472. Epub 2021 Jun 14.

Department of Neurology, Neuro-Oncology Laboratory/Clinical and Cancer Proteomics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.

Antimicrobial resistance is mostly studied by means of phenotypic growth inhibition determinations, in combination with PCR confirmations or further characterization by means of whole genome sequencing (WGS). However, the actual proteins that cause resistance such as enzymes and a lack of porins cannot be detected by these methods. Improvements in liquid chromatography (LC) and mass spectrometry (MS) enabled easier and more comprehensive proteome analysis. Read More

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Peptide profiling in cow urine reveals molecular signature of physiology-driven pathways and in-silico predicted bioactive properties.

Sci Rep 2021 Jun 14;11(1):12427. Epub 2021 Jun 14.

ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India.

Peptidomics allows the identification of peptides that are derived from proteins. Urinary peptidomics has revolutionized the field of diagnostics as the samples represent complete systemic changes happening in the body. Moreover, it can be collected in a non-invasive manner. Read More

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Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics.

Sci Rep 2021 Jun 14;11(1):12456. Epub 2021 Jun 14.

Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, Erlangen, Germany.

The family of RNA-binding proteins (RBP) functions as a crucial regulator of multiple biological processes and diseases. However, RBP function in the clinical setting of idiopathic pulmonary fibrosis (IPF) is still unknown. We developed a practical in silico screening approach for the characterization of RBPs using multi-sources data information and comparative molecular network bioinformatics followed by wet-lab validation studies. Read More

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Thermal proteome profiling reveals GPX4 as the target of the autophagy inducer conophylline.

Mol Pharmacol 2021 Jun 14. Epub 2021 Jun 14.

Pharmaceutical Frontier Research Laboratories, Japan Tobacco Inc., Japan.

Conophylline (CNP) is a vinca alkaloid extracted from the Tabernaemontana divaricata plant. It has been reported that CNP induces autophagy in a mammalian target of rapamycin (mTOR)-independent manner, thereby inhibits protein aggregation. However, the mode of action of CNP in inducing autophagy remains unknown. Read More

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Oxysterols Modify NLRP2 in Epithelial Cells, Identifying a Mediator of Ozone-induced Inflammation.

Am J Respir Cell Mol Biol 2021 Jun 14. Epub 2021 Jun 14.

University of North Carolina, Pediatrics, Chapel Hill, North Carolina, United States;

Ozone (O) is a prevalent air pollutant causing lung inflammation. Previous studies demonstrate that O oxidizes lipids, such as cholesterol, in the airway to produce oxysterols, such as secosterol-A (SecoA), which are electrophiles capable of forming covalent linkages preferentially with lysine residues and consequently modify protein function. The breadth of proteins modified by this oxysterol as well as the biological consequences in the lung are unknown. Read More

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Proteomics based drug repositioning applied to improve in vitro fertilization implantation: an artificial intelligence model.

Syst Biol Reprod Med 2021 Jun 14:1-17. Epub 2021 Jun 14.

Anaxomics Biotech S.L., Barcelona, Spain.

Embryo implantation is one of the most inefficient steps in assisted reproduction, so the identifying drugs with a potential clinical application to improve it has a strong interest. This work applies artificial intelligence and systems biology-based mathematical modeling strategies to unveil potential treatments by computationally analyzing and integrating available molecular and clinical data from patients. The mathematical models of embryo implantation computationally generated here simulate the molecular networks underneath this biological process. Read More

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Rapid 3-dimensional shape determination of globular proteins by mobility capillary electrophoresis and native mass spectrometry.

Chem Sci 2020 Apr 28;11(18):4758-4765. Epub 2020 Apr 28.

School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China

Established high-throughput proteomics methods provide limited information on the stereostructures of proteins. Traditional technologies for protein structure determination typically require laborious steps and cannot be performed in a high-throughput fashion. Here, we report a new medium throughput method by combining mobility capillary electrophoresis (MCE) and native mass spectrometry (MS) for the 3-dimensional (3D) shape determination of globular proteins in the liquid phase, which provides both the geometric structure and molecular mass information of proteins. Read More

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Proteomic analysis of pikeperch seminal plasma provides novel insight into the testicular development of domesticated fish stocks.

Animal 2021 Jun 11;15(7):100279. Epub 2021 Jun 11.

Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland.

Control of the reproduction of domesticated stocks is considered a prerequisite for aquaculture development of pikeperch. However, knowledge about the physiology of the captive pikeperch male reproductive system and the biology of semen is very limited, especially regarding protein characteristics. The aims of our study were to characterize pikeperch sperm quantity and quality parameters and to analyze changes in the proteome of the same males spawned for the first and second times. Read More

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Hypoxic responses in Oncorhynchus mykiss involve angiogenesis, lipid, and lactate metabolism, which may be triggered by the cortisol stress response and epigenetic methylation.

Comp Biochem Physiol Part D Genomics Proteomics 2021 Jun 11;39:100860. Epub 2021 Jun 11.

University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, ON L1G 0C5, Canada. Electronic address:

The incidence of hypoxia in water bodies is increasing more rapidly than aquatic life can adapt. This study aimed to determine the effects of hypoxia on fish physiology, as well as protein expression through proteomics. To do this, 40 rainbow trout were divided into normoxic control (11. Read More

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Global proteome response to Pb(II) toxicity in poplar using SWATH-MS-based quantitative proteomics investigation.

Ecotoxicol Environ Saf 2021 Jun 12;220:112410. Epub 2021 Jun 12.

Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China; International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China. Electronic address:

Lead (Pb) toxicity is a growing serious environmental pollution that threatens human health and crop productivity. Poplar, as an important economic and ecological forest species, has the characteristics of fasting growth and accumulating heavy metals, which is a powerful model plant for phytoremediation. Here, a novel label-free quantitative proteomic platform of SWATH-MS was applied to detect proteome changes in poplar seedling roots following Pb treatment. Read More

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smORFer: a modular algorithm to detect small ORFs in prokaryotes.

Nucleic Acids Res 2021 Jun 14. Epub 2021 Jun 14.

Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany.

Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Read More

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Crosstalk of the IκB Kinase with Spliced X-Box Binding Protein 1 Couples Inflammation with Glucose Metabolic Reprogramming in Epithelial-Mesenchymal Transition.

J Proteome Res 2021 Jun 14. Epub 2021 Jun 14.

Institute for Clinical and Translational Research, University of Wisconsin-Madison School of Public Health, Madison, Wisconsin 53705, United States.

Epithelial-mesenchymal transition (EMT) plays a critical role in airway injury, repair, and structural remodeling. IκB kinase (IKK)-NFκB signaling regulates late EMT-associated gene expression. However, IKK-mediated mesenchymal transition occurs earlier than NFκB/RelA subunit-dependent EMT gene expression, leading us to investigate the hypothesis that IKK plays an independent mechanism in transforming growth factor-β (TGFβ)-induced EMT. Read More

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Identification of 7 000-9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC-MS/MS.

Anal Chem 2021 Jun 14. Epub 2021 Jun 14.

Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany.

A current trend in proteomics is to acquire data in a "single-shot" by LC-MS/MS because it simplifies workflows and promises better throughput and quantitative accuracy than schemes that involve extensive sample fractionation. However, single-shot approaches can suffer from limited proteome coverage when performed by data dependent acquisition (ssDDA) on nanoflow LC systems. For applications where sample quantities are not scarce, this study shows that high proteome coverage can be obtained using a microflow LC-MS/MS system operating a 1 mm i. Read More

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Time-Dependent Analysis of pAO1 Nicotine-Related Proteome.

ACS Omega 2021 Jun 25;6(22):14242-14251. Epub 2021 May 25.

Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States.

is a soil Gram-positive nicotine-degrading microorganism (NDM) that harbors a 165 kb pAO1 catabolic megaplasmid. The nicotine catabolic genes on pAO1 have been sequenced, but not all the details on the regulation and interplay of this pathway with the general metabolism of the cell are available. To address this issue at the protein level, a time-based shotgun proteomics study was performed. Read More

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Proteomic Analysis Reveals That Metformin Suppresses PSMD2, STIP1, and CAP1 for Preventing Gastric Cancer AGS Cell Proliferation and Migration.

ACS Omega 2021 Jun 26;6(22):14208-14219. Epub 2021 May 26.

Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan.

Metformin is one of the most widely used anti-diabetic drugs in type-II diabetes treatment. The mechanism of decreasing blood glucose is believed to suppress hepatic gluconeogenesis by increasing muscular glucose uptake and insulin sensitivity. Recent studies suggest that metformin may reduce cancer risk; however, its anticancer mechanism in gastric cancers remains unclear. Read More

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Proteomics Profiling of -sulfurated Proteins in .

Bio Protoc 2021 May 5;11(9):e4000. Epub 2021 May 5.

Department of Chemistry, Indiana University, Bloomington, IN 47405 7102, USA.

Hydrogen sulfide (HS) is emerging as an important modulator in bacterial cytoprotection against the host immune response in infected animals, which may well be attributed to downstream highly oxidized sulfur species, termed reactive sulfur species (RSS), derived from HS. One mechanism by which HS/RSS may signal in the cell is through proteome -sulfuration (persulfidation), which is the conversion of protein thiols (-SH) to protein persulfides (-SSH). While several analytical methods have been developed to profile sites of protein persulfidation, few have been applied to bacterial cells. Read More

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A High-Throughput Comparative Proteomics of Milk Fat Globule Membrane Reveals Breed and Lactation Stages Specific Variation in Protein Abundance and Functional Differences Between Milk of Saanen Dairy Goat and Holstein Bovine.

Front Nutr 2021 28;8:680683. Epub 2021 May 28.

School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, China.

Large variations in the bioactivities and composition of milk fat globule membrane (MFGM) proteins were observed between Saanen dairy goat and Holstein bovine at various lactation periods. In the present study, 331, 250, 182, and 248 MFGM proteins were characterized in colostrum and mature milk for the two species by Q-Orbitrap HRMS-based proteomics techniques. KEGG pathway analyses displayed that differentially expressed proteins in colostrum involved in galactose metabolism and an adipogenesis pathway, and the differentially expressed proteins in mature milk associated with lipid metabolism and a PPAR signaling pathway. Read More

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Sphingomyelin and Medullary Sponge Kidney Disease: A Biological Link Identified by Omics Approach.

Front Med (Lausanne) 2021 26;8:671798. Epub 2021 May 26.

Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy.

Molecular biology has recently added new insights into the comprehension of the physiopathology of the medullary sponge kidney disease (MSK), a rare kidney malformation featuring nephrocalcinosis and recurrent renal stones. Pathogenesis and metabolic alterations associated to this disorder have been only partially elucidated. Plasma and urine samples were collected from 15 MSK patients and 15 controls affected by idiopathic calcium nephrolithiasis (ICN). Read More

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