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https://www.readbyqxmd.com/read/28107998/multiplex-and-accurate-quantification-of-acute-kidney-injury-biomarker-candidates-in-urine-using-protein-standard-absolute-quantification-psaq-and-targeted-proteomics
#1
Benoît Gilquin, Mathilde Louwagie, Michel Jaquinod, Alexandre Cez, Guillaume Picard, Leila El Kholy, Brigitte Surin, Jérôme Garin, Myriam Ferro, Thomas Kofman, Caroline Barau, Emmanuelle Plaisier, Pierre Ronco, Virginie Brun
There is a need for multiplex, specific and quantitative methods to speed-up the development of acute kidney injury biomarkers and allow a more specific diagnosis. Targeted proteomic analysis combined with stable isotope dilution has recently emerged as a powerful option for the parallelized evaluation of candidate biomarkers. This article presents the development of a targeted proteomic assay to quantify 4 acute kidney injury biomarker candidates in urine samples. The proteins included in the assessed panel consisted of myo-inositol oxygenase (MIOX), phosphoenolpyruvate carboxykinase 1 (PCK1), neutrophil gelatinase-associated lipocalin (NGAL) and liver fatty acid-binding protein (L-FABP)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28105913/mumal2-improving-sensitivity-in-shotgun-proteomics-using-cost-sensitive-artificial-neural-networks-and-a-threshold-selector-algorithm
#2
Fabio Ribeiro Cerqueira, Adilson Mendes Ricardo, Alcione de Paiva Oliveira, Armin Graber, Christian Baumgartner
BACKGROUND: This work presents a machine learning strategy to increase sensitivity in tandem mass spectrometry (MS/MS) data analysis for peptide/protein identification. MS/MS yields thousands of spectra in a single run which are then interpreted by software. Most of these computer programs use a protein database to match peptide sequences to the observed spectra. The peptide-spectrum matches (PSMs) must also be assessed by computational tools since manual evaluation is not practicable...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105830/improving-performance-metrics-of-ultraviolet-photodissociation-mass-spectrometry-by-selective-precursor-ejection
#3
Dustin D Holden, Jennifer S Brodbelt
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28104718/boncat-enables-time-resolved-analysis-of-protein-synthesis-in-native-plant-tissue
#4
Weslee Glenn, Shannon E Stone, Samuel H Ho, Michael J Sweredoski, Annie Moradian, Sonja Hess, Julia Bailey-Serres, David A Tirrell
Proteomic plasticity undergirds stress responses in plants, and understanding such responses requires accurate measurement of the extent to which proteins levels are adjusted to counter external stimuli. Here, we adapt bioorthogonal non-canonical amino acid tagging (BONCAT) to interrogate protein synthesis in vegetative Arabidopsis thaliana seedlings. BONCAT relies on the translational incorporation of a non-canonical amino acid (ncAA) probe into cellular proteins. In this study, the probe is the methionine surrogate azidohomoalanine (Aha), which carries a reactive azide moiety in its amino acid side chain...
January 19, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28104628/mobidb-lite-fast-and-highly-specific-consensus-prediction-of-intrinsic-disorder-in-proteins
#5
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Silvio C E Tosatto
MOTIVATION: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder...
January 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28102081/deep-coverage-of-global-protein-expression-and-phosphorylation-in-breast-tumor-cell-lines-using-tmt-10-plex-isobaric-labeling
#6
Fang-Ke Huang, Guoan Zhang, Kevin Lawlor, Arpi Nazarian, John Philip, Paul Tempst, Noah Dephoure, Thomas A Neubert
Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8706 proteins and 28186 phosphopeptides, including 7394 proteins and 23739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102078/on-peptide-selection-for-targeted-protein-quantitation
#7
Cristina Chiva, Eduard Sabidó
Targeted proteomics methods in their different flavors rely on the use of a few peptides as proxies for protein quantitation, which need to be specified either prior or after data acquisition. However, in contrast to discovery methods that use all identified peptides for a given protein to estimate its abundance, targeted proteomics methods are limited in the number of peptides that are used for protein quantitation. As only few peptides per protein are acquired or extracted in targeted experiments, the selection of peptides that are used for targeted protein quantitation becomes crucial...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102076/kinobead-and-single-shot-lc-ms-profiling-identifies-selective-pkd-inhibitors
#8
Martin Golkowski, Rama Subba Rao Vidadala, Chloe K Lombard, Hyong Won Suh, Dustin J Maly, Shao-En Ong
ATP-competitive protein kinase inhibitors are important research tools and therapeutic agents. Because there are >500 human kinases that contain highly conserved active sites, the development of selective inhibitors is extremely challenging. Methods to rapidly and efficiently profile kinase inhibitor targets in cell lysates are urgently needed to discover selective compounds and to elucidate the mechanisms of action for polypharmacological inhibitors. Here, we describe a protocol for microgram-scale chemoproteomic profiling of ATP-competitive kinase inhibitors using kinobeads...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28101936/quantitative-itraq-based-proteomic-analysis-of-rice-grains-to-assess-high-night-temperature-stress
#9
Hong-Yu Zhang, Gang Lei, Hui-Wen Zhou, Chao He, Jiang-Lin Liao, Ying-Jin Huang
Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat-tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat-tolerant and -sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database...
January 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28101252/identification-of-proteins-from-wild-cardoon-flowers-cynara-cardunculus-l-by-a-proteomic-approach
#10
Amal Ben Amira, Julien Bauwens, Edwin De Pauw, Souhail Besbes, Hamadi Attia, Frédéric Francis, Christophe Blecker
Proteomic approach was applied to identify total proteins, particularly the enzymatic content, from wild cardoon flowers. As the selection of an appropriate sample preparation method is the key for getting reliable results, two different extraction/precipitation methods (trichloroacetic acid and phenol/ammonium acetate) were tested on fresh and lyophilized flowers. After two-dimensional electrophoresis (2D-E) separations, a better protein pattern was obtained after phenol extraction from lyophilized flowers...
January 2017: Journal of Chemical Biology
https://www.readbyqxmd.com/read/28099885/oestrus-synchronisation-and-superovulation-alter-the-cervicovaginal-mucus-proteome-of-the-ewe
#11
Jessie W Maddison, Jessica P Rickard, Naomi C Bernecic, Guillaume Tsikis, Clement Soleilhavoup, Valerie Labas, Lucie Combes-Soia, Gregoire Harichaux, Xavier Druart, Tamara Leahy, Simon P de Graaf
: Although essential for artificial insemination (AI) and MOET (multiple ovulation and embryo transfer), oestrus synchronisation and superovulation are associated with increased female reproductive tract mucus production and altered sperm transport. The effects of such breeding practices on the ovine cervicovaginal (CV) mucus proteome have not been detailed. The aim of this study was to qualitatively and quantitatively investigate the Merino CV mucus proteome in naturally cycling (NAT) ewes at oestrus and mid-luteal phase, and quantitatively compare CV oestrus mucus proteomes of NAT, progesterone synchronised (P4) and superovulated (SOV) ewes...
January 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28099032/pathogenicity-genes-in-ustilaginoidea-virens-revealed-by-a-predicted-protein-protein-interaction-network
#12
Kang Zhang, Yuejiao Li, Tengjiao Li, Zhi-Gang Li, Tom Hsiang, Ziding Zhang, Wenxian Sun
Rice false smut, caused by Ustilaginoidea virens, produces significant loss in rice yield and grain quality, and has recently emerged as one of the most important rice diseases worldwide. Despite its importance in rice production, relatively few studies have been conducted to illustrate the complex interactome and the pathogenicity gene interactions. Here, a protein-protein interaction (PPI) network of U. virens was built through two well-recognized approaches, interolog and domain-domain interaction-based methods...
January 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28098164/uncovering-the-sumoylation-and-ubiquitylation-crosstalk-in-human-cells-using-sequential-peptide-immunopurification
#13
Frédéric Lamoliatte, Francis P McManus, Ghizlane Maarifi, Mounira K Chelbi-Alix, Pierre Thibault
Crosstalk between the SUMO and ubiquitin pathways has recently been reported. However, no approach currently exists to determine the interrelationship between these modifications. Here, we report an optimized immunoaffinity method that permits the study of both protein ubiquitylation and SUMOylation from a single sample. This method enables the unprecedented identification of 10,388 SUMO sites in HEK293 cells. The sequential use of SUMO and ubiquitin remnant immunoaffinity purification facilitates the dynamic profiling of SUMOylated and ubiquitylated proteins in HEK293 cells treated with the proteasome inhibitor MG132...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097710/comparative-evaluation-of-label-free-quantification-methods-for-shotgun-proteomics
#14
Julia A Bubis, Lev I Levitsky, Mark V Ivanov, Irina A Tarasova, Mikhail V Gorshkov
RATIONALE: Label-free quantification (LFQ) is a popular strategy for shotgun proteomics. A variety of LFQ algorithms have been developed recently. However, a comprehensive comparison of the most commonly used LFQ methods is still rare, in part due to a lack of clear metrics for their evaluation and an annotated and quantitatively well-characterized data set. METHODS: Five LFQ methods were compared: spectral counting based algorithms SIN , emPAI, and NSAF, and approaches relying on the extracted ion chromatogram (XIC) intensities, MaxLFQ and Quanti...
January 18, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28096085/improved-orthology-inference-with-hieranoid-2
#15
Mateusz Kaduk, Erik Sonnhammer
MOTIVATION: The initial step in many orthology inference methods is the computationally demanding establishment of all pairwise protein similarities across all analysed proteomes. The quadratic scaling with proteomes has become a major bottleneck. A remedy is offered by the Hieranoid algorithm which reduces the complexity to linear by hierarchically aggregating ortholog groups from InParanoid along a species tree. RESULTS: We have further developed the Hieranoid algorithm in many ways...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28096083/lrssl-predict-and-interpret-drug-disease-associations-based-on-data-integration-using-sparse-subspace-learning
#16
Xujun Liang, Pengfei Zhang, Lu Yan, Ying Fu, Fang Peng, Lingzhi Qu, Meiying Shao, Yongheng Chen, Zhuchu Chen
MOTIVATION: Exploring the potential curative effects of drugs is crucial for effective drug development. Previous studies have indicated that integration of multiple types of information could be conducive to discovering novel indications of drugs. However, how to efficiently identify the mechanism behind drug-disease associations while integrating data from different sources remains a challenging problem. RESULTS: In this research, we present a novel method for indication prediction of both new drugs and approved drugs...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28093892/multinucleated-giant-cells-in-the-implant-bed-of-bone-substitutes-are-foreign-body-giant-cells-new-insights-into-the-material-mediated-healing-process
#17
Mike Barbeck, Patrick Booms, Ronald Unger, Verena Hoffmann, Robert Sader, Charles James Kirkpatrick, Shahram Ghanaati
In addition to macrophages, multinucleated giant cells (MNGCs) are involved in the tissue reaction to a variety of biomaterials. Especially in the case of bone substitute materials it has been assumed that the MNGCs are osteoclasts, based on the chemical and physical similarity of many materials to the calcified matrix and the bony environment in which they are used. However, many studies indicate that these cells belong to the cell line of the foreign body giant cells (FBGCs), which are of "inflammatory origin", although they have been shown to possess both a pro- and also anti-inflammatory phenotype...
January 17, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28093409/deuterater-a-tool-for-quantifying-peptide-isotope-precision-and-kinetic-proteomics
#18
Bradley C Naylor, Michael T Porter, Elise Wilson, Adam Herring, Spencer Lofthouse, Austin Hannemann, Stephen R Piccolo, Alan L Rockwood, John C Price
MOTIVATION: Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don't access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28093123/synthesis-of-stable-isotopically-labeled-peptides-with-filter-assisted-enzymatic-labeling-for-the-diagnosis-of-hepatitis-b-virus-infection-utilizing-mass-spectrometry-based-proteomics-strategy
#19
Hsing-Fen Tsai, He-Hsuan Hsiao
A facile method for the preparation of stable isotopically labeled peptides was developed by means of filter-assisted tryptic (16)O/(18)O water labeling, which could be directly applied to the determination of hepatitis B virus infection from human serum with tandem mass spectrometry. Tryptic peptides of hepatitis B surface antigen or hepatitis B e antigen from different subtypes of hepatitis B virus were synthesized with traditional solid-phase peptide synthesis as potential biomarkers. Trypsin catalyzed oxygen-18 exchange at their amidated c-terminus of arginine or lysine residue...
March 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28092050/microwestern-arrays-for-systems-level-analysis-of-sh2-domain-containing-proteins
#20
Mark F Ciaccio, Richard B Jones
The Microwestern Array (MWA) method combines the scalability and miniaturization afforded by the Reverse Phase Lysate Array (RPLA) approach with the electrophoretic separation characteristic of the Western blot. This technology emulates the creation of an array of small Western blots on a single sheet of nitrocellulose allowing for the sensitive and quantitative measurement of hundreds of proteins from hundreds of cell lysates with minimal cost and maximal accuracy, precision, and reproducibility. The MWA is a versatile technology that can be easily configured for purposes such as antibody screening, cell signaling network inference, protein modification/phenotype regression analysis, and genomic/proteomic relationships...
2017: Methods in Molecular Biology
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