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Proteomics

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https://www.readbyqxmd.com/read/27928909/using-proteomics-to-discover-novel-biomarkers-for-fatty-liver-development-and-response-to-cb1r-antagonist-treatment-in-an-obese-mouse-model
#1
Chin-Chang Chen, Tzung-Yan Lee, Ching-Fai Kwok, Yung-Pei Hsu, Kuang-Chung Shih, Yan-Jie Lin, Low-Tone Ho
Over activity of cannabinoid receptor type 1 (CB1R) plays a key role in increasing the incidence of obesity-induced nonalcoholic fatty liver disease. Tissue proteome analysis has been applied to investigate the bioinformatics regarding the mode of action and therapeutic mechanism. The aim of this study was to explore the potential pathways altered with CB1R in obesity-induced fatty liver. Male C57BL/6 mice were fed either a standard chow diet (STD) or a high-fat diet (HFD) with or without 1-week treatment of CB1R inverse agonist AM251 at 5 mg/kg...
December 8, 2016: Proteomics
https://www.readbyqxmd.com/read/27928908/striking-against-bioterrorism-with-advanced-proteomics-and-reference-methods
#2
Jean Armengaud
The intentional use by terrorists of biological toxins as weapons has been of great concern for many years. Amongst the numerous toxins produced by plants, animals, algae, fungi and bacteria, ricin is one of the most scrutinized by the media because it has already been used in biocrimes and acts of bioterrorism. Improving the analytical toolbox of national authorities to monitor these potential bioweapons all at once is of the utmost interest. Tandem mass spectrometry allows their absolute quantitation and exhibits advantageous sensitivity, discriminative power, multiplexing possibilities, and speed...
December 8, 2016: Proteomics
https://www.readbyqxmd.com/read/27928884/building-proteomic-tool-boxes-to-monitor-mhc-class-i-and-class-ii-peptides
#3
REVIEW
Frances-Rose Schumacher, Lélia Delamarre, Suchit Jhunjhunwala, Zora Modrusan, Qui T Phung, Joshua E Elias, Jennie R Lill
Major histocompatibility complex Class I (MHCI) and Class II (MHCII) presented peptides powerfully modulate T cell immunity and play a vital role in generating effective anti-tumor and anti-viral immune responses in mammals. Characterizing these MHCI or MHCII presented peptides can help generate therapeutic treatments, afford information on T cell mediated biomarkers, provide insight into disease progression, and reduce adverse anti-drug side effects from engineered biotherapeutics. Here, we explore the tools and techniques commonly employed to discover both MHCI and MHCII presented peptides...
December 8, 2016: Proteomics
https://www.readbyqxmd.com/read/27896924/detailed-tail-proteomic-analysis-of-axolotl-ambystoma-mexicanum-using-an-mrna-seq-reference-database
#4
Turan Demircan, Ilknur Keskin, Seda Nilgun Dumlu, Nilufer Ayturk, Mahmut Erhan Avsaroglu, Emel Akgun, Gurkan Ozturk, Ahmet Tarik Baykal
Salamander Axolotl has been emerging as an important model for stem cell research due to its powerful regenerative capacity. Several advantages, such as the high capability of advanced tissue, organ and appendages regeneration, promote Axolotl as an ideal model system to extend our current understanding on the mechanisms of regeneration. Acknowledging the common molecular pathways between amphibians and mammals, there is a great potential to translate the messages from Axolotl research to mammalian studies...
November 29, 2016: Proteomics
https://www.readbyqxmd.com/read/27891773/cigarette-smoke-alters-the-secretome-of-lung-epithelial-cells
#5
Alessandra Mossina, Christina Lukas, Juliane Merl-Pham, Franziska E Uhl, Kathrin Mutze, Andrea Schamberger, Claudia Staab-Weijnitz, Jie Jia, Ali Ö Yildirim, Melanie Königshoff, Stefanie M Hauck, Oliver Eickelberg, Silke Meiners
Cigarette smoke is the most relevant risk factor for the development of lung cancer and chronic obstructive pulmonary disease (COPD). Many of its more than 4500 chemicals are highly reactive thereby altering protein structure and function. Here, we used subcellular fractionation coupled to label-free quantitative mass spectrometry to globally assess alterations in the proteome of different compartments of lung epithelial cells upon exposure to cigarette smoke extract. Proteomic profiling of the human alveolar-derived cell line A549 revealed the most pronounced changes within the cellular secretome with preferential downregulation of proteins involved in wound healing and extracellular matrix (ECM) organization...
November 28, 2016: Proteomics
https://www.readbyqxmd.com/read/27891772/twoplex-12-13-c6-aniline-stable-isotope-and-linkage-specific-sialic-acid-labelling-2d-lc-ms-workflow-for-quantitative-n-glycomics
#6
Simone Albrecht, Stefan Mittermayr, Josh Smith, Silvia Millán Martín, Margaret Doherty, Jonathan Bones
Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-ToF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing...
November 28, 2016: Proteomics
https://www.readbyqxmd.com/read/27883257/determining-the-binding-affinities-of-prostate-specific-antigen-to-lectins-spr-and-microarray-approaches
#7
Pavel Damborský, Martina Zámorová, Jaroslav Katrlík
Prostate cancer (PCa) is one of the most common newly diagnosed cancer among men and we focused on its traditional biomarker, prostate-specific antigen (PSA), using targeted glycomics-based strategies. The aberrant glycosylation pattern of PSA may serve as valuable tool for improving PCa diagnosis including its early-stage. In the present work we evaluated the usability of two techniques, surface plasmon resonance and protein microarray assay, for the study and characterization of interactions of PSA (both free and complexed) with 6 lectins (SNA, ConA, RCA, AAL, WGA and MAA II)...
November 24, 2016: Proteomics
https://www.readbyqxmd.com/read/27880036/protein-phosphotyrosine-proteome-profiling-by-superbinder-sh2-domain-affinity-purification-mass-spectrometry-ssh2-ap-ms
#8
Jiefei Tong, Biyin Cao, Gregory D Martyn, Jonathan R Krieger, Paul Taylor, Bradley Yates, Sachdev S Sidhu, Shawn S C Li, Xinliang Mao, Michael F Moran
Recently, "superbinder" SH2 domain variants with three amino acid substitutions (sSH2) were reported to have 100-fold or greater affinity for protein-phosphotyrosine (pY) than natural SH2 domains. Here we report a protocol in which His-tagged Src sSH2 efficiently captures pY-peptides from protease-digested HeLa cell total protein extracts. Affinity purification of pY-peptides by this method shows little bias for pY-proximal amino acid sequences, comparable to that achieved by using antibodies to pY, but with equal or higher yield...
November 23, 2016: Proteomics
https://www.readbyqxmd.com/read/27880033/a-comparative-proteomic-analysis-reveals-important-proteins-for-the-fertilization-and-early-embryonic-development-of-the-oyster-crassostrea-gigas
#9
Xiaohong Huang, Pin Huan, Baozhong Liu
Molluscan development involves important features that are important to understanding not only molluscan ontogeny but also animal evolution. To gain insight into the gamete proteome and protein function in fertilization and early development, we analyzed the proteomes of unfertilized oocytes and early embryos (2/4-cell stage) of the Pacific oyster, Crassostrea gigas. An oocyte reference map containing 116 protein spots, of which 69 were identified, revealed a high abundance of vitellogenin (Vg)-derived protein spots...
November 23, 2016: Proteomics
https://www.readbyqxmd.com/read/27860250/transcription-factor-proteomics-tools-applications-and-challenges
#10
REVIEW
Jovan Simicevic, Bart Deplancke
Transcription factors (TFs) are a family of DNA-binding proteins whose gene regulatory capabilities are of vital importance in defining the molecular state of a cell. Despite their biological significance, our understanding of TF behavior and function is still limited. This is because we have so far mostly relied on gene expression data to approximate TF protein levels given that the latter information has been notoriously difficult to obtain due to the relatively low expression levels of many TFs. However, significant advances in mass spectrometry technologies combined with the development of sensitive methodologies aimed at detecting TFs are now allowing a transition from a predominantly qualitative to a quantitative protein landscape...
November 18, 2016: Proteomics
https://www.readbyqxmd.com/read/27862927/a-robotic-protocol-for-high-throughput-processing-of-samples-for-selected-reaction-monitoring-assays
#11
Min Zhu, Pingbo Zhang, Minghui Geng-Spyropoulos, Ruin Moaddel, Richard D Semba, Luigi Ferrucci
Selected reaction monitoring mass spectrometry (SRM-MS) is a sensitive and accurate method for quantification of targeted proteins in biological specimens. However, the sample throughput and reliability of this technique is limited by the complexity of sample preparation, as well as instrumentation and data processing. Modern robotic equipment allows for rapid and accurate processing of large number of samples and makes SRM-MS assay applicable in epidemiological studies. Herein, we describe an automated sample processing platform developed in the context of an SRM-MS protocol for the assay of complement factor H protein and its variants in human plasma...
November 15, 2016: Proteomics
https://www.readbyqxmd.com/read/27862981/standardization-of-sample-homogenization-for-mosquito-identification-using-an-innovative-proteomic-tool-based-on-protein-profiling
#12
Amira Nebbak, Alexandra C Willcox, Idir Bitam, Didier Raoult, Philippe Parola, Lionel Almeras
The rapid spread of vector-borne diseases demands the development of an innovative strategy for arthropod monitoring. The emergence of MALDI-TOF MS as a rapid, low-cost and accurate tool for arthropod identification is revolutionizing medical entomology. However, as MS spectra from an arthropod can vary according to the body part selected, the sample homogenization method used and the mode and duration of sample storage, standardization of protocols is indispensable prior to the creation and sharing of an MS reference spectra database...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27862975/purification-of-soluble-hla-class-i-complexes-from-human-serum-or-plasma-deliver-high-quality-immuno-peptidomes-required-for-biomarker-discovery
#13
Danilo Ritz, Andreas Gloger, Dario Neri, Tim Fugmann
Soluble human leukocyte antigen class I (sHLA)-peptide complexes have been suggested to play a role in the modulation of immune responses and in immune evasion of cancer cells. The set of peptides eluted from sHLA molecules could serve as biomarker for the monitoring of patients with cancer or other conditions. Here, we describe an improved sHLA peptidomics methodology resulting in the identification of 1816 to 2761 unique peptide sequences from triplicate analyses of serum or plasma taken from three healthy donors...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27862958/nicotine-induced-protein-expression-profiling-reveals-mutually-altered-proteins-across-four-human-cell-lines
#14
Joao A Paulo, Steven P Gygi
Mass spectrometry-based proteomic strategies can profile the expression level of proteins in response to external stimuli. Nicotine affects diverse cellular pathways, however, the nicotine-induced alterations on the global proteome across human cell lines have not been fully elucidated. We measured perturbations in protein levels resulting from nicotine treatment in four cell lines - HEK, HeLa, PaSC, and SH-SY5Y- in a single experiment using tandem mass tags (TMT10-plex) and high-resolution mass spectrometry...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27862954/automation-of-prm-dependent-d3-leu-tracer-enrichment-in-hdl-to-study-the-metabolism-of-apoa-i-lcat-and-other-apolipoproteins
#15
Lang Ho Lee, Allison B Andraski, Brett Pieper, Hideyuki Higashi, Frank M Sacks, Masanori Aikawa, Sasha A Singh
We developed an automated quantification workflow for PRM-enabled detection of D3-Leu labeled apoA-I in HDL isolated from humans. Subjects received a bolus injection of D3-Leu and blood was drawn at seven time points over three days. HDL was isolated and separated into six size fractions for subsequent proteolysis and PRM analysis for the detection of D3-Leu signal from ∼0.03 to 0.6 % enrichment. We implemented an intensity-based quantification approach that takes advantage of high resolution/accurate mass PRM scans to identify the D3-Leu 2HM3 ion from non-specific peaks...
November 9, 2016: Proteomics
https://www.readbyqxmd.com/read/27860397/comparison-of-sample-preparation-techniques-for-large-scale-proteomics
#16
Miljan Kuljanin, Dylan Z Dieters-Castator, David A Hess, Lynne-Marie Postovit, Gilles A Lajoie
Numerous workflows exist for large scale bottom-up proteomics, many of which achieve exceptional proteome depth. Herein, we evaluated the performance of several commonly used sample preparation techniques for proteomic characterization of HeLa lysates (unfractionated in-solution digests, SDS-PAGE coupled with in-gel digestion, gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) technology, SCX StageTips and High-/Low-pH reversed phase fractionation (HpH)). HpH fractionation was found to be superior in terms of proteome depth (>8400 proteins detected) and fractionation efficiency compared to other techniques...
November 9, 2016: Proteomics
https://www.readbyqxmd.com/read/27860232/the-proteomes-of-the-human-eye-a-highly-compartmentalized-organ
#17
Gilbert S Omenn
Proteomics has now published a series of Dataset Briefs on the EyeOme from the HUPO Human Proteome Project with high-quality analyses of the proteomes of these compartments of the human eye: retina, iris, ciliary body, retinal pigment epithelium/choroid, retrobulbar optic nerve, and sclera, with 3436, 2929, 2867, 2755, 2711, and 1945 proteins, respectively. These proteomics resources represent a useful starting point for a broad range of research aimed at developing preventive and therapeutic interventions for the various causes of blindness...
November 9, 2016: Proteomics
https://www.readbyqxmd.com/read/27775233/an-enlarged-cell-wall-proteome-of-arabidopsis-thaliana-rosettes
#18
Vincent Hervé, Harold Duruflé, Hélène San Clemente, Cécile Albenne, Thierry Balliau, Michel Zivy, Christophe Dunand, Elisabeth Jamet
Plant cells are surrounded by cell walls playing many roles during development and in response to environmental constraints. Cell walls are mainly composed of polysaccharides (cellulose, hemicelluloses and pectins), but they also contain proteins which are critical players in cell wall remodelling processes. Today, the cell wall proteome of Arabidopsis thaliana, a major dicot model plant, comprises more than 700 proteins predicted to be secreted (CWPs) identified in different organs or in cell suspension cultures...
October 24, 2016: Proteomics
https://www.readbyqxmd.com/read/27775219/towards-comprehensive-and-quantitative-proteomics-for-diagnosis-and-therapy-of-human-disease
#19
Paolo Cifani, Alex Kentsis
Given superior analytical features, mass spectrometry proteomics is well suited for the basic investigation and clinical diagnosis of human disease. Modern mass spectrometry enables detailed functional characterization of the pathogenic biochemical processes, as achieved by accurate and comprehensive quantification of proteins and their regulatory chemical modifications. Here, we describe how high-accuracy mass spectrometry in combination with high-resolution chromatographic separations can be leveraged to meet these analytical requirements in a mechanism-focused manner...
October 24, 2016: Proteomics
https://www.readbyqxmd.com/read/27774731/impact-of-phosphoproteomics-in-the-translation-of-kinase-targeted-therapies
#20
Pedro Casado, Maruan Hijazi, David Britton, Pedro R Cutillas
Signalling pathways driven by protein and lipid kinases are altered in most human diseases. Therefore, pharmacological inhibitors of cell signalling are one of the most intensively pursued therapeutic approaches for the treatment of diseases such as cancer, neurodegeneration and metabolic syndromes. Phosphoproteomics is a technique that measures the products of kinase activities and, with the appropriate bioinformatics techniques, the methodology can also provide measures of kinase pathway activation and network circuitry...
October 24, 2016: Proteomics
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