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MS and proteomics

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https://read.qxmd.com/read/30781766/optimisation-of-protein-extraction-from-medicinal-cannabis-mature-buds-for-bottom-up-proteomics
#1
Delphine Vincent, Simone Rochfort, German Spangenberg
Medicinal cannabis is used to relieve the symptoms of certain medical conditions, such as epilepsy. Cannabis is a controlled substance and until recently was illegal in many jurisdictions. Consequently, the study of this plant has been restricted. Proteomics studies on Cannabis sativa reported so far have been primarily based on plant organs and tissues other than buds, such as roots, hypocotyl, leaves, hempseeds and flour. As far as we know, no optimisation of protein extraction from cannabis reproductive tissues has been attempted...
February 13, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://read.qxmd.com/read/30781614/involvement-of-actin-cytoskeletal-components-in-breast-cancer-cell-fusion-with-human-mesenchymal-stroma-stem-like-cells
#2
Catharina Melzer, Juliane von der Ohe, Ralf Hass
Cell fusion as a rare event was observed following the co-culture of human MDA-MB-231cherry breast cancer cells or benign neoplastic MCF10Acherry breast epithelial cells together with different mesenchymal stroma/stem-like cells (MSCGFP ) cultures, respectively, resulting in the generation of double-fluorescing hybrid cells. Analysis of potential molecular mechanisms for the formation of cancer hybrid cells revealed cytoskeletal components, including F-actin. Thus, a sub-lethal concentration of cytochalasin D, which blocks elongation of actin filaments, was able to significantly reduce cancer hybrid cell formation...
February 18, 2019: International Journal of Molecular Sciences
https://read.qxmd.com/read/30781434/morpho-physiological-and-proteomic-analyses-of-eucalyptus-camaldulensis-as-a-bioremediator-in-copper-polluted-soil-in-saudi-arabia
#3
Modhi O Alotaibi, Afrah E Mohammed, Taghreed A Almutairi, Mudawi M Elobeid
The present investigation aimed to assess the impact of copper (Cu) stress on the physiological and proteomic behavior of Eucalyptus camaldulensis . E. camaldulensis is likely a potential phytoremediator in areas vulnerable to Cu contamination, such as the industrial areas of Riyadh. To realize this objective, young seedlings of E. camaldulensis were potted in an open area with soil comprised of clay and sand. Different doses of Cu (30, 50, and 100 µM) were applied to the plants as CuSO₄.5H₂O for 6 weeks...
February 15, 2019: Plants (Basel, Switzerland)
https://read.qxmd.com/read/30781343/trends-in-the-design-of-new-isobaric-labeling-reagents-for-quantitative-proteomics
#4
REVIEW
Remigiusz Bąchor, Mateusz Waliczek, Piotr Stefanowicz, Zbigniew Szewczuk
Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups...
February 15, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://read.qxmd.com/read/30779583/depletion-of-high-molecular-mass-proteins-for-the-identification-of-small-proteins-and-short-open-reading-frame-encoded-peptides-in-cellular-proteomes
#5
Liam Cassidy, Philipp T Kaulich, Andreas Tholey
The identification of small proteins and peptides (below ca. 100 to 150 amino acids) in complex biological samples is hampered by the dominance of higher molecular weight proteins. On the other hand, the increasing knowledge about alternative or short open reading frames creates a need for methods that allow the existence of the corresponding gene products to be proven in proteomics experiments. We present an acetonitrile-based precipitation methodology which depletes the majority of proteins above ca. 15 kDa...
February 19, 2019: Journal of Proteome Research
https://read.qxmd.com/read/30778366/unveiling-kiwifruit-metabolite-and-protein-changes-in-the-course-of-postharvest-cold-storage
#6
Anna Maria Salzano, Giovanni Renzone, Anatoly P Sobolev, Virginia Carbone, Milena Petriccione, Donatella Capitani, Monica Vitale, Gianfranco Novi, Nicola Zambrano, Maria Silvia Pasquariello, Luisa Mannina, Andrea Scaloni
Actinidia deliciosa cv. Hayward fruit is renowned for its micro- and macronutrients, which vary in their levels during berry physiological development and postharvest processing. In this context, we have recently described metabolic pathways/molecular effectors in fruit outer endocarp characterizing the different stages of berry physiological maturation. Here, we report on the kiwifruit postharvest phase through an integrated approach consisting of pomological analysis combined with NMR/LC-UV/ESI-IT-MSn - and 2D-DIGE/nanoLC-ESI-LIT-MS/MS-based proteometabolomic measurements...
2019: Frontiers in Plant Science
https://read.qxmd.com/read/30778115/urinary-proteome-signature-of-renal-cysts-and-diabetes-syndrome-in-children
#7
Pierbruno Ricci, Pedro Magalhães, Magdalena Krochmal, Martin Pejchinovski, Erica Daina, Maria Rosa Caruso, Laura Goea, Iwona Belczacka, Giuseppe Remuzzi, Muriel Umbhauer, Jens Drube, Lars Pape, Harald Mischak, Stéphane Decramer, Franz Schaefer, Joost P Schanstra, Silvia Cereghini, Petra Zürbig
Renal Cysts and Diabetes Syndrome (RCAD) is an autosomal dominant disorder caused by mutations in the HNF1B gene encoding for the transcriptional factor hepatocyte nuclear factor-1B. RCAD is characterized as a multi-organ disease, with a broad spectrum of symptoms including kidney abnormalities (renal cysts, renal hypodysplasia, single kidney, horseshoe kidneys, hydronephrosis), early-onset diabetes mellitus, abnormal liver function, pancreatic hypoplasia and genital tract malformations. In the present study, using capillary electrophoresis coupled to mass spectrometry (CE-MS), we investigated the urinary proteome of a pediatric cohort of RCAD patients and different controls to identify peptide biomarkers and obtain further insights into the pathophysiology of this disorder...
February 18, 2019: Scientific Reports
https://read.qxmd.com/read/30776612/beneficial-effects-of-coomassie-staining-on-proteomic-analysis-employing-page-separation-followed-with-whole-gel-slicing-in-gel-digestion-and-quantitative-lc-ms-ms
#8
Ya Jin, Meiling Wen, Qi Yuan, Jun Zhang, Wen Tan
Proteomic analysis by combining PAGE separation, gel slicing and slice-by-slice in-gel digestion and LC-MS/MS has been frequently reported in recent years. Since the MS analysis would provide identities and quantities of the proteins along the whole lane, gel visualization by dye staining could be skipped to save time and labor. In this work, we examined the effects of CBB R-250 staining on the performance of the method and the results showed actually better results were obtained with CBB staining than without, both in nondenaturing PAGE and SDS-PAGE...
February 11, 2019: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://read.qxmd.com/read/30776456/optimisation-of-protein-extraction-for-in-depth-profiling-of-the-cereal-grain-proteome
#9
Utpal Bose, James A Broadbent, Keren Byrne, Shihab Hasan, Crispin A Howitt, Michelle L Colgrave
Cereal grain proteomics can provide valuable information regarding plant growth, nutritional status, adaptation to environmental stresses, and the role that grain proteins play in health disorders, such as coeliac disease. In this study liquid chromatography-mass spectrometry was used to compare the barley proteome after extraction using seven protocols, with and without defatting and protein precipitation steps that aimed to remove interfering secondary metabolites. Tris-HCl and urea buffers yielded 1405 and 1483 proteins (~79% overlap) from barley (cv Sloop)...
February 15, 2019: Journal of Proteomics
https://read.qxmd.com/read/30774579/characterization-of-the-plasma-proteome-of-nonhuman-primates-during-ebola-virus-disease-or-melioidosis-a-host-response-comparison
#10
Michael D Ward, Ernst E Brueggemann, Tara Kenny, Raven E Reitstetter, Christopher R Mahone, Sylvia Trevino, Kelly Wetzel, Ginger C Donnelly, Cary Retterer, Robert B Norgren, Rekha G Panchal, Travis K Warren, Sina Bavari, Lisa H Cazares
Background: In-depth examination of the plasma proteomic response to infection with a wide variety of pathogens can assist in the development of new diagnostic paradigms, while providing insight into the interdependent pathogenic processes which encompass a host's immunological and physiological responses. Ebola virus (EBOV) causes a highly lethal infection termed Ebola virus disease (EVD) in primates and humans. The Gram negative non-spore forming bacillus Burkholderia pseudomallei ( Bp ) causes melioidosis in primates and humans, characterized by severe pneumonia with high mortality...
2019: Clinical Proteomics
https://read.qxmd.com/read/30774578/quantitative-proteomic-characterization-of-lung-tissue-in-idiopathic-pulmonary-fibrosis
#11
Yaqiong Tian, Hui Li, Yujuan Gao, Chuanmei Liu, Ting Qiu, Hongyan Wu, Mengshu Cao, Yingwei Zhang, Hui Ding, Jingyu Chen, Hourong Cai
Background: Idiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease. IPF is characterized by excessive accumulation of the extracellular matrix (ECM) in the alveolar parenchyma and progressive lung scarring. The pathogenesis of IPF and whether the ECM involved in the process remain unknown. Methods: To identify potential treatment target and ECM associated proteins that may be involved in the development of IPF, we employed isobaric tag for relative and absolute quantitation (iTRAQ) combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to examine protein expression in lung tissues from IPF patients...
2019: Clinical Proteomics
https://read.qxmd.com/read/30773324/discovery-of-aaa-protease-substrates-through-trapping-approaches
#12
REVIEW
Jui-Yun Rei Liao, Klaas J van Wijk
Proteases play essential roles in cellular proteostasis. Mechanisms through which proteases recognize their substrates are often hard to predict and therefore require experimentation. In vivo trapping allows systematic identification of potential substrates of proteases, their adaptors, and chaperones. This combines in vivo genetic modifications of proteolytic systems, stabilized protease-substrate interactions, affinity enrichments of trapped substrates, and mass spectrometry (MS)-based identification. In vitro approaches, in which immobilized protease components are incubated with isolated cellular proteome, complement this in vivo approach...
February 14, 2019: Trends in Biochemical Sciences
https://read.qxmd.com/read/30772974/-biomarkers-screening-for-viral-myocarditis-through-proteomics-analysis-of-plasma-exosomes
#13
Z L Zhao, S Du, S X Shen, P Luo, S K Ding, G G Wang, L X Wang
Objective: To compare and analyze the differentially expressed plasma exosomic proteome between healthy control group (Control group) and viral myocarditis group (VMC group) to search for biomarkers that maybe used for early diagnosis of VMC. Methods: Fifty plasma samples of Control group and VMC group were collected respectively from Henan Provincial People's Hospital (from January 2016 to December 2017), and then 5 samples (1 ml) of each group were selected randomly, after exosomes extraction with ultra-centrifugation, difference gel electrophoresis (DIGE) was used to isolate the total proteins, and then the protein spots with more than 2-fold changes between VMC and Control group were picked up after the software analysis, afterward, the varied proteins were identified by MALDI-TOF/TOF mass spectrometry...
January 29, 2019: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://read.qxmd.com/read/30772661/comparative-proteomic-identification-of-capacitation-and-noncapacitation-swamp-buffalo-spermatozoa
#14
Zhen Hou, Qiang Fu, Yulin Huang, Pengfei Zhang, Fumei Chen, Mingxing Li, Zhuangzhuang Xu, Shun Yao, Dongrong Chen, Ming Zhang
To investigate the proteomic profiling in buffalo spermatozoa before and after capacitation, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with Tandem Mass Tag (TMT) labeling strategy was applied. As a result, 1461 proteins were identified, 93 of them were found to be differentially expressed (>1.5-fold), including 52 up-regulated proteins and 41 down-regulated proteins during sperm capacitation. 88 out of 93 proteins were annotated and classified. Gene ontology (GO) analysis revealed that most of the differently expressed proteins (DEPs) were involved in the Biological Process of transport, cytoskeleton organization, sexual reproduction, and spermatogenesis...
February 7, 2019: Theriogenology
https://read.qxmd.com/read/30771950/mass-spectrometry-based-proteomic-approach-for-the-screening-of-butyrylcholinesterase-adduct-formation-with-organophosphates
#15
Yaroslav Dubrovskii, Ekaterina Murashko, Olga Chuprina, Petr Beltyukov, Andrey Radilov, Nikolay Solovyev, Vladimir Babakov
Organophosphates' toxic effect causes covalent binding to serine-198 in the active site of human plasma butyrylcholinesterase (BChE) with loss of enzymatic function (covalent inhibition). Mass spectrometric detection of modified FGESAGAAS peptide at the active site is a powerful exposure biomarker tool. The aim of this study was to develop mass spectrometry-based method for BChE adduct formation screening, avoiding the use of standard peptides. Immunomagnetic separation of proteins from plasma was optimized...
May 15, 2019: Talanta
https://read.qxmd.com/read/30771357/somatic-proteome-of-haemonchus-contortus
#16
Tao Wang, Guangxu Ma, Ching-Seng Ang, Pasi K Korhonen, Rong Xu, Shuai Nie, Anson V Koehler, Richard J Simpson, David W Greening, Gavin E Reid, Nicholas A Williamson, Robin B Gasser
Currently, there is a dearth of proteomic data to underpin fundamental investigations of parasites and parasitism at the molecular level. Here, using a high throughput LC-MS/MS-based approach, we undertook the first reported comprehensive, large-scale proteomic investigation of the barber's pole worm (Haemonchus contortus) - one of the most important parasitic nematodes of livestock animals worldwide. In total, 2487 unique H. contortus proteins representing different developmental stages/sexes (i.e. eggs, (L3s and L4s, female (Af) and male (Am) adults) were identified and quantified with high confidence...
February 13, 2019: International Journal for Parasitology
https://read.qxmd.com/read/30770655/intra-surgical-protein-layer-on-titanium-arthroplasty-explants-from-the-big-twelve-to-the-implant-proteome
#17
Marcus Jäger, Herbert P Jennissen, Marcel Haversath, André Busch, Thomas Grupp, Andrea Sowislok, Monika Herten
PURPOSE: Aseptic loosening in total joint replacement due to insufficient osteointegration is an unsolved problem in orthopaedics. The purpose of our study was to obtain a picture of the initial protein adsorption layer on femoral endoprosthetic surfaces as the key to the initiation of osseointegration. EXPERIMENTAL DESIGN: This paper describes the first study of femoral stem explants from patients for proteome analysis of the primary protein layer. After 2 min...
February 15, 2019: Proteomics. Clinical Applications
https://read.qxmd.com/read/30767403/mass-spectrometric-evaluation-of-upstream-and-downstream-process-influences-on-host-cell-protein-patterns-in-biopharmaceutical-products
#18
Heiner Falkenberg, Daniel Michael Waldera-Lupa, Martin Vanderlaan, Thomas Schwab, Kurt Krapfenbauer, Joey Michael Studts, Thomas Flad, Thomas Waerner
For production of different monoclonal antibodies (mAbs), biopharmaceutical companies often use related upstream and downstream manufacturing processes. Such platforms are typically characterized regarding influence of upstream and downstream process (DSP) parameters on critical quality attributes (CQAs). CQAs must be monitored strictly by an adequate control strategy. One such process-related CQA is the content of host cell protein (HCP) which is typically analyzed by immunoassay methods (e.g. HCP-ELISA). The capacity of the immunoassay to detect a broad range of HCPs, relevant for the individual mAb-production process should be proven by orthogonal proteomic methods such as 2D gel electrophoresis or mass spectrometry (MS)...
February 15, 2019: Biotechnology Progress
https://read.qxmd.com/read/30765875/brivanib-in-combination-with-notch3-silencing-shows-potent-activity-in-tumour-models
#19
Catia Giovannini, Anna Maria Salzano, Michele Baglioni, Monica Vitale, Andrea Scaloni, Nicola Zambrano, Ferdinando Antonio Giannone, Francesco Vasuri, Antonia D'Errico, Gianluca Svegliati Baroni, Luigi Bolondi, Laura Gramantieri
BACKGROUND: Sorafenib is the first targeted agent proven to improve survival of patients with advanced hepatocellular carcinoma (HCC) and it has been used in first line treatments with heterogeneous response across patients. Most of the promising agents evaluated in first-line or second-line phase III trials for HCC failed to improve patient survival. The absence of molecular characterisation, including the identification of pathways driving resistance might be responsible for these disappointing results...
February 15, 2019: British Journal of Cancer
https://read.qxmd.com/read/30765861/interferon-stimulated-gene-15-modulates-cell-migration-by-interacting-with-rac1-and-contributes-to-lymph-node-metastasis-of-oral-squamous-cell-carcinoma-cells
#20
Yu-Lin Chen, Wan-Lin Wu, Chuan-Wei Jang, Yi-Chen Yen, Ssu-Han Wang, Fang-Yu Tsai, Ying-Ying Shen, Ya-Wen Chen
In an effort to understand the underlying mechanisms of lymph node metastasis in oral squamous cell carcinoma (OSCC), through in vivo selection, LN1-1 cells were previously established from OEC-M1 cells and showed enhanced lymphangiogenesis and lymphatic metastasis capabilities. In the current study, we use a stable isotope labeling with amino acids in cell culture (SILAC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic platform to compare LN1-1 to OEC-M1 cells. Interferon-stimulated gene 15 (ISG15) was found highly expressed in LN1-1 cells...
February 14, 2019: Oncogene
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