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https://www.readbyqxmd.com/read/28448532/a-selected-reaction-monitoring-mass-spectrometric-assessment-of-biomarker-candidates-diagnosing-large-cell-neuroendocrine-lung-carcinoma-by-the-scaling-method-using-endogenous-references
#1
Tetsuya Fukuda, Masaharu Nomura, Yasufumi Kato, Hiromasa Tojo, Kiyonaga Fujii, Toshitaka Nagao, Yasuhiko Bando, Thomas E Fehniger, György Marko-Varga, Haruhiko Nakamura, Harubumi Kato, Toshihide Nishimura
Selected reaction monitoring mass spectrometry (SRM-MS) -based semi-quantitation was performed to assess the validity of 46 selected candidate proteins for specifically diagnosing large-cell neuroendocrine lung carcinoma (LCNEC) and differentiating it from other lung cancer subtypes. The scaling method was applied in this study using specific SRM peak areas (AUCs) derived from the endogenous reference protein that normalizes all SRM AUCs obtained for the candidate proteins. In a screening verification study, we found that seven out of the 46 candidate proteins were statistically significant for the LCNEC phenotype, including 4F2hc cell surface antigen heavy chain (4F2hc/CD98) (p-ANOVA ≤ 0...
2017: PloS One
https://www.readbyqxmd.com/read/28448054/lipid-droplet-isolation-for-quantitative-mass-spectrometry-analysis
#2
Kathrin Rösch, Marcel Kwiatkowski, Hartmut Schlüter, Eva Herker
Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of virion morphogenesis. Quantitative lipid droplet proteome analysis can be used to identify proteins that localize to or are displaced from lipid droplets under conditions such as virus infections. Here, we describe a protocol that has been successfully used to characterize the changes in the lipid droplet proteome following infection with HCV. We use Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) and thus label the complete proteome of one population of cells with "heavy" amino acids to quantitate the proteins by mass spectrometry...
April 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448026/lerlic-ms-ms-for-in-depth-characterization-and-quantification-of-glutamine-and-asparagine-deamidation-in-shotgun-proteomics
#3
Xavier Gallart-Palau, Aida Serra, Siu Kwan Sze
Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples...
April 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28444712/the-urinary-microbiome-and-its-contribution-to-lower-urinary-tract-symptoms-ici-rs-2015
#4
REVIEW
Marcus J Drake, Nicola Morris, Apostolos Apostolidis, Mohammad S Rahnama'i, Julian R Marchesi
AIMS: The microbiome is the term used for the symbiotic microbial colonisation of healthy organs. Studies have found bacterial identifiers within voided urine which is apparently sterile on conventional laboratory culture, and accordingly there may be health and disease implications. METHODS: The International Consultation on Incontinence Research Society (ICI-RS) established a literature review and expert consensus discussion focussed on the increasing awareness of the urinary microbiome, and potential research priorities...
April 2017: Neurourology and Urodynamics
https://www.readbyqxmd.com/read/28444347/fluxomics-links-cellular-functional-analyses-to-whole-plant-phenotyping
#5
Christophe Salon, Jean-Christophe Avice, Sophie Colombié, Martine Dieuaide-Noubhani, Karine Gallardo, Christian Jeudy, Alain Ourry, Marion Prudent, Anne-Sophie Voisin, Dominique Rolin
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping...
April 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28441545/targeted-mass-spectrometry-an-emerging-powerful-approach-to-unblock-the-bottleneck-in-phosphoproteomics
#6
REVIEW
Nerea Osinalde, Kerman Aloria, Miren J Omaetxebarria, Irina Kratchmarova
Following the rapid expansion of the proteomics field, the investigation of post translational modifications (PTM) has become extremely popular changing our perspective of how proteins constantly fine tune cellular functions. Reversible protein phosphorylation plays a pivotal role in virtually all biological processes in the cell and it is one the most characterized PTM up to date. During the last decade, the development of phosphoprotein/phosphopeptide enrichment strategies and mass spectrometry (MS) technology has revolutionized the field of phosphoproteomics discovering thousands of new site-specific phosphorylations and unveiling unprecedented evidence about their modulation under distinct cellular conditions...
April 17, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28439861/sample-preparation-protocols-for-protein-abundance-acetylome-and-phosphoproteome-profiling-of-plant-tissues
#7
Gaoyuan Song, Maxwell R McReynolds, Justin W Walley
Peptide mass spectrometry is an invaluable technique to globally quantify the proteome. Central to proteome profiling are efficient methods to extract proteins, digest proteins into peptides, and enrich for posttranslationally modified peptides prior to mass spectrometry. In this chapter, we describe methods to extract proteins, process them into peptides, and optionally enrich for phospho- and acetyl-peptides prior to analysis by mass spectrometry.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439280/insights-on-structure-and-function-of-a-late-embryogenesis-abundant-protein-from-amaranthus-cruentus-an-intrinsically-disordered-protein-involved-in-protection-against-desiccation-oxidant-conditions-and-osmotic-stress
#8
Alma L Saucedo, Eric E Hernández-Domínguez, Luis A de Luna-Valdez, Angel A Guevara-García, Abraham Escobedo-Moratilla, Esaú Bojorquéz-Velázquez, Federico Del Río-Portilla, Daniel A Fernández-Velasco, Ana P Barba de la Rosa
Late embryogenesis abundant (LEA) proteins are part of a large protein family that protect other proteins from aggregation due to desiccation or osmotic stresses. Recently, the Amaranthus cruentus seed proteome was characterized by 2D-PAGE and one highly accumulated protein spot was identified as a LEA protein and was named AcLEA. In this work, AcLEA cDNA was cloned into an expression vector and the recombinant protein was purified and characterized. AcLEA encodes a 172 amino acid polypeptide with a predicted molecular mass of 18...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439035/the-regulation-function-and-detection-of-protein-acetylation-in-bacteria
#9
Valerie J Carabetta, Ileana M Cristea
N(ε)-lysine acetylation is now recognized as an abundant post-translational modification (PTM) that influences many essential biological pathways. Advancements in mass spectrometry-based proteomics have led to the discovery that bacteria contain hundreds of acetylated proteins, contrary to the prior notion of rare acetylation events in bacteria. Although the mechanisms that regulate protein acetylation are still not fully defined, it is understood that this modification is finely-tuned via both enzymatic and non-enzymatic mechanisms...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28438806/emerging-affinity-based-proteomic-technologies-for-large-scale-plasma-profiling-in-cardiovascular-disease
#10
REVIEW
J Gustav Smith, Robert E Gerszten
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets...
April 25, 2017: Circulation
https://www.readbyqxmd.com/read/28438675/integrating-cell-biology-and-proteomic-approaches-in-plants
#11
Tomáš Takáč, Olga Šamajová, Jozef Šamaj
Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science...
April 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28438609/novel-replicons-and-trans-encapsidation-systems-for-hepatitis-c-virus-proteins-live-imaging-and-virus-host-interaction-proteomics
#12
Ovidiu Vlaicu, Tudor Selescu, Florin Pastrama, Cristian Munteanu, Laura Riva, Jean Dubuisson, Yves Rouille, Costin-Ioan Popescu
Proteomics and imaging techniques are used more and more in tandem to investigate the virus-host interaction. Herein we present novel replicons, methods and trans-encapsidation systems suitable for determination of Hepatitis C Virus (HCV) proteins interactomes and live imaging of viral proteins dynamics in HCV cell culture (HCVcc) system. To identify endogenous factors involved in the HCV life cycle, we constructed full-length functional replicons with affinity purification (AP) tags fused to NS2 and NS5A proteins...
April 21, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28438560/longitudinal-investigation-of-salivary-proteomic-profiles-in-the-development-of-early-childhood-caries
#13
Shuang Ao, Xiangyu Sun, Xiangru Shi, Xin Huang, Feng Chen, Shuguo Zheng
OBJECTIVES: To investigate differentially expressed salivary peptides in the development of early childhood caries (ECC) in 3-4 year-old children. MATERIALS AND METHODS: Eighty-two caries-free children at baseline were followed-up for 1year, during which period 15 of them had developed ECC (GroupC), whilst another 15 cases out of the 31 individuals who remained healthy were marked as Group H. Stimulated whole saliva samples were collected at 0, 6 and 12 months, and analyzed using weak cation exchange magnetic beads combined with matrix assisted laser desorption/ionization time-of-flight mass spectrometry...
April 21, 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/28438116/the-predictive-nature-of-transcript-expression-levels-on-protein-expression-in-adult-human-brain
#14
Amy L Bauernfeind, Courtney C Babbitt
BACKGROUND: Next generation sequencing methods are the gold standard for evaluating expression of the transcriptome. When determining the biological implications of such studies, the assumption is often made that transcript expression levels correspond to protein levels in a meaningful way. However, the strength of the overall correlation between transcript and protein expression is inconsistent, particularly in brain samples. RESULTS: Following high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses of adult human brain samples, we compared the correlation in the expression of transcripts and proteins that support various biological processes, molecular functions, and that are located in different areas of the cell...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28437088/hilaq-a-novel-strategy-for-newly-synthesized-protein-quantification
#15
Yuanhui Ma, Daniel B McClatchy, Salim Barkallah, William W Wood, John R Yates Iii
Here we describe a new strategy, HILAQ (Heavy Isotope Labeled Azidohomoalanine Quantification), to rapidly quantify the molecular vulnerability profile to oxytosis, which is an oxidative stress-induced programed cell death pathway that has been reported to be involved in aging and neurodegenerative diseases. HILAQ was able to quantify 1,962 Newly Synthesized Proteins (NSPs) after 1h pulse labeling in HEK293T cell line, while 353 proteins were quantified using the previously published QuaNCAT protocol. HILAQ was successfully applied to the HT22 oxytosis model...
April 24, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28436665/intra-and-interskeletal-proteome-variations-in-fresh-and-buried-bones
#16
Noemi Procopio, Andrew T Chamberlain, Michael Buckley
Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Here, we evaluated the proteomes obtained from five distinct subsamples of different skeletal elements from buried pig carcasses to ascertain the extent of variation within and between individuals...
April 24, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28435053/in-depth-analysis-of-the-synaptic-plasma-membrane-proteome-of-small-hippocampal-slices-using-an-integrated-approach
#17
Rui Qiao, Shuiming Li, Mi Zhou, Penghui Chen, Zhao Liu, Min Tang, Jian Zhou
Comprehensive knowledge of the synaptic plasma membrane (SPM) proteome of a distinct brain region in a defined pathological state would greatly advance the understanding of the underlying biology of synaptic plasticity. The development of innovative approaches for studying the SPM proteome of small brain tissues is highly desired. This study presents a suitable protocol that integrates biotinylation-based affinity capture of cell surface-exposed proteins, isolation of synaptosomes, and biochemical extraction of SPM proteins from biotinylated hippocampal slices...
April 20, 2017: Neuroscience
https://www.readbyqxmd.com/read/28434875/covalent-protein-labeling-at-glutamic-acids
#18
Pablo Martín-Gago, Eyad K Fansa, Michael Winzker, Sandip Murarka, Petra Janning, Carsten Schultz-Fademrecht, Matthias Baumann, Alfred Wittinghofer, Herbert Waldmann
Covalent labeling of amino acids in proteins by reactive small molecules, in particular at cysteine SH and lysine NH groups, is a powerful approach to identify and characterize proteins and their functions. However, for the less-reactive carboxylic acids present in Asp and Glu, hardly any methodology is available. Employing the lipoprotein binding chaperone PDE6δ as an example, we demonstrate that incorporation of isoxazolium salts that resemble the structure and reactivity of Woodward's reagent K into protein ligands provides a novel method for selective covalent targeting of binding site carboxylic acids in whole proteomes...
April 13, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28434225/in-depth-proteome-coverage-by-improving-efficiency-for-membrane-proteome-analysis
#19
Qun Zhao, Fei Fang, Yichu Shan, Zhigang Sui, Baofeng Zhao, Zhen Liang, Lihua Zhang, YuKui Zhang
Although great achievement has been made in the mapping of human proteome, the efficiency of sample preparation still needs to be improved, especially for membrane proteins. Herein, we presented a novel method to deepen proteome coverage by the sequential extraction of proteins using urea and 1-dodecyl-3- methylimidazoliumchloride (C12Im-Cl). With such a strategy, the commonly lost hydrophobic proteins by 8 M urea extraction could be further recovered by C12Im-Cl, as well as the suppression effect of high abundance soluble proteins could be decreased...
April 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28432464/insights-into-autosomal-dominant-polycystic-kidney-disease-by-quantitative-mass-spectrometry-based-proteomics
#20
REVIEW
Britta Diedrich, Jörn Dengjel
Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenetic disorder that is caused by mutations in the genes PKD1 and PKD2 encoding polycystin-1 and polycystin-2, respectively. Polycystin-1 and -2 form a complex, interact with several proteins involved in signal transduction and localize to discrete subcellular positions, most importantly the primary cilium. Whereas the causative mutations leading to ADPKD are known, the underlying deregulated cellular pathways are not well understood. In the current review, we introduce state-of-the-art mass spectrometry (MS)-based proteomic techniques and summarize their use in kidney and ADPKD research...
April 21, 2017: Cell and Tissue Research
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