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Johannes Stadlmann, David M Hoi, Jasmin Taubenschmid, Karl Mechtler, Josef M Penninger
SugarQb ( is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS data-sets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F-resistant N-glycopeptides from mouse embryonic stem cells. The analysis of intact glycopeptides highlights unexpected technical limitations to PNGase F-dependent glycoproteomic workflows at the proteome level, and warrants a critical re-interpretation of seminal data-sets in the context of N-glycosylation-site prediction...
May 18, 2018: Proteomics
Simone Sidoli
Histones are the most abundant protein family in the cells of complex organisms such as mammals and, together with DNA, they define the backbone of chromatin. Histone PTMs are key players of chromatin biology, as they function as anchors for proteins that bind and modulate chromatin readout, including gene expression. Middle-down mass spectrometry (MS) has been optimized for about 10 years to study histone N-terminal tails, but it has been rarely applied to identify the role of co-existing histone marks in biology...
May 9, 2018: Proteomics
Xiang Li, Matt D Dun, Sam Faulkner, Hubert Hondermarck
Recent breakthrough discoveries have highlighted the stimulatory role of nerves in cancer initiation and progression, through the release of neurotransmitters and growth factors by nerve terminals in the tumor microenvironment. Intriguingly, neuroproteins such as neuronal membrane proteins, synaptic proteins, neurotransmitters and neurotrophic growth factors as well as their corresponding receptors, to name only a few, are frequently found in proteomic analyses of cancer tissues external to the brain and central nervous system...
May 9, 2018: Proteomics
Megan H Wright
The dynamic proteome plays numerous roles in the interactions of microbes - whether they are invading pathogens or symbiotic organisms - and their hosts. Host and microbe sense, respond and manipulate each other's biology via a multitude of mechanisms, resulting in alterations in protein expression or post-translational modification that influence protein localisation, activity or binding partners. The intrinsic, temporal and spatial complexity of multi-species systems makes identifying the molecular players challenging...
May 9, 2018: Proteomics
Yuxin Chen, Sen Wang, Jia Jia, Xinyu Tian, Hongpan Xu, Mingzhe Ning, Bing Bai
Long-term storage of protein samples for transportation is a challenge in the field of mass spectrometric analysis because the low temperature condition is not easy to be maintained. Here we introduce a simple method to preserve proteins at room temperature for at lease one month. In this method, the protein sample is run shortly into a polyacrylamide gel which is then excised after Coomassie staining. The protein gel band is then dehydrated by 100% acetonitrile for three times and kept in the 100% acetonitrile for storage at the room temperature...
May 8, 2018: Proteomics
Harshavardhan Budamgunta, Volodimir Olexiouk, Walter Luyten, Karin Schildermans, Evelyne Maes, Kurt Boonen, Gerben Menschaert, Geert Baggerman
Bio-active peptides are involved in the regulation of most physiological processes in the body. Classical bio-active peptides (CBAPs) are cleaved from a larger precursor protein and stored in secretion vesicles from which they are released in the extracellular space. Recently, another non-classical type of bio-active peptides (NCBAPs) have gained interest. These typically are not secreted but instead appear to be translated from short open reading frames (sORF) and released directly into the cytoplasm. In contrast to CBAPs, these peptides are involved in the regulation of intra-cellular processes such as transcriptional control, calcium handling and DNA repair...
April 30, 2018: Proteomics
Sonali R Bhagwat, Krishnan Hajela, Amit Kumar
Proteolysis is an irreversible post-translational modification process, characterized by highly precise yet stable cleavage of proteins. Downstream events in signaling processes are reliant on proteolysis triggered by the protease activity. Studies indicate that abnormal proteolytic activity may lead to the manifestation of diseased conditions. Therefore, characterization of proteases may provide clues to understand their role in fundamental cellular processes like cellular growth, differentiation, apoptosis, and survival...
April 30, 2018: Proteomics
Jan Arends, Marcena Griego, Nikolas Thomanek, Claudia Lindemann, Blanka Kutscher, Helmut E Meyer, Franz Narberhaus
Controlling the cellular abundance and proper function of proteins by proteolysis is a universal process in all living organisms. In Escherichia coli, the ATP-dependent Lon protease is crucial for protein quality control and regulatory processes. To understand how diverse substrates are selected and degraded, unbiased global approaches are needed. We employed a quantitative Super-SILAC mass spectrometry approach and compared the proteomes of a lon mutant and a strain producing the protease to discover Lon-dependent physiological functions...
April 30, 2018: Proteomics
Chao Du, Gilles P van Wezel
Natural products (NPs) are a major source of compounds for the medical, agricultural and biotechnological industry. Many of these compounds are of microbial origin, and in particular from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multi-omics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity...
April 30, 2018: Proteomics
Liran Komov, Dganit Melamed Kadosh, Eilon Barnea, Elena Milner, Ayellet Hendler, Arie Admon
While antigen processing and presentation by the major histocompatibility complex class I molecules (MHC-I) have been extensively studied, a question arises as to whether the level of MHC-I expression is limited by the supply of peptide-receptive (empty) MHC molecules, or by the availability of peptide ligands for loading. To this end, we evaluated the MHC peptidomes resulting from exposure of human breast cancer cells (MCF-7) to interferons. Although all four HLA allotypes of the MCF-7 cells (HLA-A*02:01, B*18, B*44, and C*5) present peptides of similar lengths and C-termini, which should be processed similarly by the proteasome and by the antigen processing and presentation chaperones, the interferons induced differential modulation of the HLA-A, B and C peptidomes...
April 29, 2018: Proteomics
Maria João Sebastião, Rute Pereira, Margarida Serra, Patrícia Gomes-Alves, Paula Marques Alves
Cardiac Fibroblasts (CFs) are one of the main cell populations in the heart and play important roles in tissue homeostasis and myocardial fibrosis. The study of these cells has been hampered by the lack of reliable membrane markers: none of the antigens currently used for characterization and isolation of CFs is unique for this cell type. This issue has also raised doubts regarding a distinct identity of cardiac fibroblasts when comparing to other myocardium cell populations with similar morphologies. In this work, we report a comprehensive description and functional analysis of human CFs (hCFs) membrane-enriched fraction proteome by advanced mass spectrometry-based proteomic tools...
April 25, 2018: Proteomics
Joseph Rothnagel, Gerben Menschaert
No abstract text is available yet for this article.
April 25, 2018: Proteomics
Xiaolu Zhang, Huaipu Chang, Zhaoming Dong, Yan Zhang, Dongchao Zhao, Lin Ye, Qingyou Xia, Ping Zhao
The silk gland of silkworm produces silk proteins during larval development. Many studies have long focused on the silk gland of the fifth instar larvae, but few have investigated this gland at other larval stages. In the present study, the silk gland proteomes of the fourth instar and fourth molt were analyzed using liquid chromatography-tandem mass spectrometry. In total, 2654 proteins were identified from the silk gland. High abundance of ribosomal proteins and RR-motif chitin-binding proteins were identified during day 2 of the fourth instar (IV-2) larval developmental stage, and the expression of cuticular proteins analogous to peritrophin (CPAP)-motif chitin-binding proteins was higher during the fourth molt (IV-M)...
April 24, 2018: Proteomics
Cristina Russo, Emily E L Lewis, Lucy Flint, Malcolm R Clench
A 3D cell culture is an artificially created environment in which cells are permitted to grow/interact with their surroundings in all three dimensions. Derived from 3D cell culture, organoids are generally small-scale constructs of cells that are fabricated in the laboratory to serve as 3D representations of in vivo tissues and organs. Due to regulatory, economic and societal issues concerning the use of animals in scientific research it seems clear that the use of 3D cell culture and organoids in for example early stage studies of drug efficacy and toxicity will increase...
April 24, 2018: Proteomics
Dezhi Kong, Xiaolin Tian, Yunshan Li, Saihang Zhang, Yiru Cheng, Lifang Huo, Huanhuan Ma, Zuxiao Yang, Leiming Ren, Zhang Mingquan, Wei Zhang
Ginseng, the active ingredients of which are ginsenosides, is the most popular herbal medicine and has potential merit in the treatment of cerebral disorders. To better understand the function of Ginseng in the cerebral system, we examined changes in the protein expression profiles of synaptosomes extracted from the cerebral cortical and hippocampal tissues of rats administered a high or low dose of Ginseng for two weeks. More than five thousand proteins belonging to synaptosomes were simultaneously identified and quantitated by an approach combining tandem mass tags with two-dimensional liquid chromatography-mass spectrometry (LC-MS)...
April 23, 2018: Proteomics
Tingting Jiang, Michael E Hoover, Matthew V Holt, Michael A Freitas, Alan G Marshall, Nicolas L Young
Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis...
April 17, 2018: Proteomics
Joao A Paulo, Steven P Gygi
Nicotinic acetylcholine receptors (nAChR), the primary cell surface targets of nicotine, have implications in various neurological disorders. Here we investigate the proteome-wide effects of nicotine on human haploid cell lines (wildtype HAP1 and α7KO-HAP1) to address differences in nicotine-induced protein abundance profiles between these cell lines. We performed an SPS-MS3-based TMT10-plex experiment arranged in a 2-3-2-3 design with two replicates for the untreated samples and three for the treated samples for each cell line...
April 16, 2018: Proteomics
Joao A Paulo, Mark P Jedrychowski, Edward T Chouchani, Lawrence Kazak, Steven P Gygi
Nicotine is a major addictive compound in tobacco and a component of smoking-related products, such as e-cigarettes. Once internalized, nicotine can perturb many cellular pathways and can induce alterations in proteins across different cell types, however the mechanisms thereof remain undetermined. We hypothesize that both tissue-specific and global protein abundance alterations result from nicotine exposure. As such, we present the first proteome analysis of multiple tissues from nicotine-exposed mice. We treat mice via oral administration of nicotine at 200μg/mL in drinking water for 21 days...
April 16, 2018: Proteomics
Katelyn E Connelly, Victoria Hedrick, Tiago Jose Paschoal Sobreira, Emily C Dykhuizen, Uma K Aryal
Analysis of protein complexes provides insights into how the ensemble of expressed proteome is organized into functional units. While there have been advances in techniques for proteome-wide profiling of cytoplasmic protein complexes, information about human nuclear protein complexes are very limited. To close this gap, we combined native size exclusion chromatography (SEC) with label-free quantitative mass spectrometry profiling to characterize hundreds of nuclear protein complexes isolated from human glioblastoma multiforme (GBM) T98G cells...
April 14, 2018: Proteomics
Noelia Ruzafa, Xandra Pereiro, Marlen F Lepper, Stefanie M Hauck, Elena Vecino
The retinal Müller glial cells, like other types of glial cells, can enhance the survival and activity of neurons, especially of retinal ganglion cells (RGCs), which are the neurons affected in diseases such as glaucoma, diabetes and retinal ischemia. It has been demonstrated that Müller glia release neurotrophic factors that support RGC survival, yet many of these factors remain to be elucidated. To define these neurotrophic factors, we adopted a quantitative proteomic approach aiming at identifying neuroprotective proteins...
April 12, 2018: Proteomics
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