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Ying Zhang, Xi Wang, Dan Cui, Jun Zhu
The human whole saliva is a vital body fluid to study the physiology and pathology of oral cavity. As a powerful technique for biomarker discovery, mass spectrometry-based proteomic strategy has been introduced to saliva analysis and identified hundreds of proteins and N-glycosylation sites. However, there still lacks of quantitative analysis, which is necessary for biomarker screening and biological researches. In this study, we established an integrated workflow by the combination of stable isotope dimethyl labeling, HILIC enrichment and high resolution mass spectrometry for both quantification of global proteome and N-glycoproteome of human saliva from oral ulcer patients...
October 20, 2016: Proteomics
Fernando J Sialana, Peter Gulyassy, Peter Májek, Evelina Sjöstedt, Viktor Kis, André C Müller, Elena L Rudashevskaya, Jan Mulder, Keiryn L Bennett, Gert Lubec
The molecular composition of synaptic signal transduction machineries shapes synaptic neurotransmission. The repertoire of receptors, transporters and channels (RTCs) comprises major signaling events in the brain. RTCs are conventionally studied by candidate immunohistochemistry and biochemistry, which are low throughput with resolution greatly affected by available immunoreagents and membrane interference. Therefore, a comprehensive resource of synaptic brain RTCs is still lacking. In particular, studies on the detergent-soluble synaptosomal fraction, known to contain transporters and channels, are limited...
October 19, 2016: Proteomics
Mariaconcetta Varano, Marco Gaspari, Angela Quirino, Giovanni Cuda, Maria Carla Liberto, Alfredo Focà
Ochrobactrum anthropi is a gram-negative rod belonging to the Brucellaceae family, able to colonize a variety of environments, and actually reported as a human opportunistic pathogen. Despite its low virulence, the bacterium causes a growing number of hospital-acquired infections mainly, but not exclusively, in immunocompromised patients. The aim of this study was to obtain an overview of the global proteome changes occurring in O. anthropi in response to different growth temperatures, in order to achieve a major understanding of the mechanisms by which the bacterium adapts to different habitats and to identify some potential virulence factors...
October 18, 2016: Proteomics
Xingwang Jia, Jing Chen, Shisheng Sun, Weiming Yang, Shuang Yang, Punit Shah, Naseruddin Hoti, Bob Veltri, Hui Zhang
Clinical management of prostate cancer remains a significant challenge due to the lack of available tests for guiding treatment decisions. The blood Prostate-Specific Antigen (PSA) test has facilitated early detection and intervention of prostate cancer. However, blood PSA levels are less effective in distinguishing aggressively from indolent prostate cancers and other benign prostatic diseases. Thus, the development of novel approaches specific for prostate cancer that can differentiate aggressively from indolent disease remains an urgent medical need...
October 17, 2016: Proteomics
Leslie Muller, Luc Fornecker, Alain Dorsselaer, Sarah Cianférani, Christine Carapito
Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide-gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD)...
October 17, 2016: Proteomics
Xiao Chen, Yin Kwan Wong, Jigang Wang, Jianbin Zhang, Yew-Mun Lee, Han-Ming Shen, Qingsong Lin, Zi-Chun Hua
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible...
October 10, 2016: Proteomics
Xiaojing Yan, Liangliang Sun, Guijie Zhu, Olivia F Cox, Norman J Dovichi
A tryptic digest generated from Xenopus laevis fertilized embryos was fractionated by reversed phase liquid chromatography. One set of 30 fractions was analyzed by 100-min CZE-ESI-MS/MS separations (50 hr total instrument time), and a second set of 15 fractions was analyzed by 3-hr UPLC-ESI-MS/MS separations (45 hr total instrument time). CZE-MS/MS produced 70% as many protein IDs (4,134 vs. 5,787) and 60% as many peptide IDs (22,535 vs. 36,848) as UPLC-MS/MS with similar instrument time (50 h vs. 45 h) but with 50 times smaller total consumed sample amount (1...
October 10, 2016: Proteomics
Un-Beom Kang, Jarrod A Marto
Leucine-rich repeat kinase 2 (LRRK2) is a large multi-domain protein that is expressed in many tissues and participates in numerous biological pathways. Mutations in LRRK2 are recognized as genetic risk factors for familial Parkinson's disease (PD) and may also represent causal factors in the more common sporadic form of PD. The structure of LRRK2 comprises a combination of GTPase, kinase, and scaffolding domains. This functional diversity, combined with a potentially central role in genetic and idiopathic PD motivates significant effort to further credential LRRK2 as a therapeutic target...
October 10, 2016: Proteomics
Aki Manninen, Markku Varjosalo
Individual cells in multicellular organisms constantly explore their microenvironment, or niche, to obtain spatial information that is used to regulate cell behavior to maintain tissue integrity. The extracellular matrix (ECM) is an important source of such spatial information. Binding of the integrin family receptors to the ECM triggers formation of integrin adhesion complexes (IACs) which link the ECM network to cellular cytoskeleton via remarkably large multiprotein complexes collectively referred to as the integrin adhesome...
October 9, 2016: Proteomics
Bastien Dalzon, Hélène Diemer, Véronique Collin-Faure, Sarah Cianférani, Thierry Rabilloud, Catherine Aude-Garcia
The physiology of cells cultured in vitro depends obviously on the external conditions, including the nutrients present in the culture medium. In order to test the influence of this parameter, J774 macrophages grown either in RPMI or in DMEM were compared by a combination of targeted analyses and a proteomic approach. The two media differ in their glucose, amino acids and vitamins concentrations, but there was no significant differences in the cell cycle nor in the percentage of phagocytic cells in both media, although the phagocytic capacity (i...
October 9, 2016: Proteomics
Nathan P Manes, Aleksandra Nita-Lazar
Bottom-up targeted proteomics using selected reaction monitoring (SRM) is a powerful analytical technology, but it requires the development of SRM assays, which is a complex procedure. Whereas proteome-wide SRM assays have recently been developed for a small number of species, this is not so for the mouse. In this issue, Percy et al 1 report the development of hundreds of mouse SRM assays. Their development required shotgun MS to identify proteotypic peptides, synthesis and LC-MS characterization of peptide standards, and inter-laboratory SRM to robustly assess the quality of the assays...
October 8, 2016: Proteomics
Elisabeth Govaert, Katleen Van Steendam, Ellen Scheerlinck, Liesbeth Vossaert, Paulien Meert, Martina Stella, Sander Willems, Laura De Clerck, Maarten Dhaenens, Dieter Deforce
Extracting histones from cells is the first step in studies that aim to characterize histones and their post-translational modifications (hPTMs) with MS. In the last decade, label-free quantification is more frequently being used for MS-based histone characterization. However, many histone extraction protocols were not specifically designed for label-free MS. While label-free quantification has its advantages, it is also very susceptible to technical variation. Here, we adjust an established histone extraction protocol according to general label-free MS guidelines with a specific focus on minimizing sample handling...
October 8, 2016: Proteomics
Chadwick M Hales, Eric B Dammer, Qiudong Deng, Duc M Duong, Marla Gearing, Juan C Troncoso, Madhav Thambisetty, James J Lah, Joshua M Shulman, Allan I Levey, Nicholas T Seyfried
Despite a key role of amyloid-beta (Aβ) in Alzheimer's disease (AD), mechanisms that link Aβ plaques to tau neurofibrillary tangles and cognitive decline still remain poorly understood. The purpose of this study was to quantify proteins in the sarkosyl-insoluble brain proteome correlated with Aβ and tau insolubility in the asymptomatic phase of AD (AsymAD) and through mild cognitive impairment (MCI) and symptomatic AD. Employing label-free mass spectrometry based proteomics, we quantified 2,711 sarkosyl-insoluble proteins across the prefrontal cortex from 35 individual cases representing control, AsymAD, MCI and AD...
October 8, 2016: Proteomics
Yasser El-Manzalawy, Elyse E Munoz, Scott E Lindner, Vasant Honavar
Accurate and comprehensive identification of surface exposed proteins (SEPs) in parasites is a key step in developing novel subunit vaccines. However, the reliability of mass spectrometry-based high-throughput methods for proteome-wide mapping of SEPs continues to be limited due to high rates of false positives (i.e., proteins mistakenly identified as surface exposed) as well as false negatives (i.e., SEPs not detected due to low expression or other technical limitations). We propose a framework called PlasmoSEP for the reliable identification of SEPs using a novel semi-supervised learning algorithm that combines SEPs identified by high-throughput experiments and expert annotation of high-throughput data to augment labeled data for training a predictive model...
October 7, 2016: Proteomics
Mariette Matondo, Marlène Marcellin, Karima Chaoui, Marie-Pierre Bousquet-Dubouch, Anne Gonzalez-de-Peredo, Bernard Monsarrat, Odile Burlet-Schiltz
The ubiquitin-proteasome pathway (UPP) plays a critical role in the degradation of proteins implicated in cell cycle control, signal transduction, DNA damage response, apoptosis and immune response. Proteasome inhibitors can inhibit the growth of a broad spectrum of human cancer cells by altering the balance of intracellular proteins. However, the targets of these compounds in acute myeloid leukemia (AML) cells have not been fully characterized. Herein, we combined large-scale quantitative analysis by SILAC-MS and targeted quantitative proteomic analysis in order to identify proteins regulated upon proteasome inhibition in two AML cell lines displaying different stages of maturation: immature KG1a cells and mature U937 cells...
October 6, 2016: Proteomics
Oleg V Krokhin, Vic Spicer
The emergence of data independent quantitative LC-MS/MS analysis protocols further highlights the importance of high quality reproducible chromatographic procedures. Knowing, controlling and being able to predict the effect of multiple factors that alter peptide RP-HPLC separation selectivity is critical to successful data collection for the construction of ion libraries. Proteomic researchers have often regarded RP-HPLC as a "black box", while vast amounts of research on peptide separation is readily available...
October 4, 2016: Proteomics
Marvin Dörries, Lars Wöhlbrand, Ralf Rabus
The marine sulfate-reducing bacterium Desulfobacterium autotrophicum HRM2 belongs to the deltaproteobacterial family Desulfobacteraceae and stands out for its capacity of facultative chemolithoautotrophic growth (next to heterotrophy). Here, proteomics-driven metabolic reconstruction was based on a combination of 2D DIGE, shotgun proteomics and analysis of the membrane protein-enriched fraction applied to 8 different substrate adaptation conditions (7 aliphatic compounds plus H2 /CO2 ). In total 1,344 different proteins were identified (∼27% of the 4,947 genome-predicted) from which a complex metabolic network was reconstructed consisting of 136 proteins (124 detected; ∼91%)...
October 4, 2016: Proteomics
Alex-Ane Mathieu, Emma Ohl-Séguy, Marie-Line Dubois, Dominique Jean, Christine Jones, François Boudreau, François-Michel Boisvert
Studying cell differentiation and transformation allows a better understanding of the mechanisms involved in the initiation and the evolution of cancer. The role of proteins which participate in these processes is dependent on their location within the cell. Determining the subcellular localization of proteins or the changes in localization is, therefore, paramount in elucidating their role. Using quantitative mass spectrometry, we characterized the protein expression and subcellular localization of nearly 5,000 proteins from seven different colorectal cancer (CRC) cell lines, as well as normal colon fibroblasts and intestinal epithelial cells...
September 30, 2016: Proteomics
Andrew J Percy, Sarah A Michaud, Armando Jardim, Nicholas J Sinclair, Suping Zhang, Yassene Mohammed, Andrea L Palmer, Darryl B Hardie, Juncong Yang, Andre M LeBlanc, Christoph H Borchers
The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards...
September 30, 2016: Proteomics
Zhen Gao, Chengjun Zhang, Meng Luo, Yusen Wu, Shuyan Duan, Jiefa Li, Lei Wang, Shiren Song, Wenping Xu, Shiping Wang, Caixi Zhang, Chao Ma
Pears are one of the most popular nutrient-rich fruits in the world. The pear core and mesocarp have significantly different metabolism, although they display similar profiles. Most strikingly, the core is more acidic in taste. Our results showed that there is more titrated acid but lower total soluble solids in the core compared to the mesocarp, and the content of citric acid was more than 17-fold higher in the core compared to the mesocarp at the ripening stage. Proteomics was used to investigate the difference between core and mesocarp tissues during 'Cuiguan' pear ripening...
September 30, 2016: Proteomics
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