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Proteomics

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https://www.readbyqxmd.com/read/28230319/depletion-of-abundant-human-serum-proteins-by-per-se-imprinted-cryogels-based-on-sample-heterogeneity
#1
Chun Yang, Ya-Ru Liu, Yan Zhang, Jian Wang, Li-Li Tian, Ya-Nan Yan, Wei-Qin Cao, Yu-Yang Wang
Macroporous cryogels were prepared and used to deplete abundant proteins. It was accomplished based on the sample heterogeneity rather than any exogenous assistance. Human serum was added in monomer solutions to synthesize molecularly imprinted polymers (MIPs); therein some abundant proteins were imprinted in the polyacrylamide cryogels. Meanwhile the rare components remained aqueous. Chromatography and electrophoresis showed that albumin, serotransferrin and most globulins were depleted by columns packed with the MIPs...
February 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28225217/proteomic-analysis-of-the-cullin4b-interactome-using-proximity-dependent-biotinylation-in-living-cells
#2
Hailong Zhang, Shupeng Li, Pingting Liu, Frankie H F Lee, Albert H C Wong, Fang Liu
Cullin 4B (CUL4B) mutations have been implicated in mental retardation and dopamine-related behaviors due to disruptions in their interaction with Cullin-RING E3 ligases (CRLs). Thus, further identification of CUL4B substrates can increase the knowledge of protein homeostasis and illuminate the role of CUL4B in neuropsychiatric disease. However, the transient nature of the coupling between CUL4B and its substrates is difficult to detect in vivo using current approaches, thus hampers efforts to investigate functions of CRLs within unperturbed living systems...
February 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28225203/identification-of-interacting-proteins-of-the-tafve-protein-involved-in-spike-development-in-bread-wheat
#3
Yong-Sheng Zheng, Yu-Qing Lu, Ying-Ying Meng, Rong-Zhi Zhang, Han Zhang, Jia-Mei Sun, Mu-Mu Wang, Li-Hui Li, Ru-Yu Li
FVE/MSI4 plays important roles in determining flowering time in Arabidopsis. However, its function is unexplored in wheat. In the present study, Co-IP and nano-LC-MS/MS were used to identify TaFVE-interacting or associated proteins. Altogether 89 differentially expressed proteins showed the same down-regulated expression trends as TaFVE in wheat line 5660M. Among them, 62 proteins were further predicted to be involved in the interaction network of TaFVE and 11 proteins have been shown to be potential TaFVE interactors based on curated databases and experimentally determined in other species by the STRING...
February 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28221718/quantitative-analysis-of-shigella-flexneri-protein-expression-under-acid-stress
#4
Kaiwen Yu, Zhen Wang, Fan Zhou, Jiezhang Jiang, Yanhua Liu, Mo Hu, Xiaoyun Liu
As an important foodborne pathogen, Shigella flexneri can cause widespread enteric infection with bacteria as few as hundreds. This is, at least in part, attributed to its robust anti-acid strategies because passage through the highly acidic human digestive tract is a prerequisite for successful bacterial infection. Nevertheless, our understanding of these mechanisms and the impact of acid stress on Shigella protein expression still remains largely incomplete. Herein we conducted a proteomic survey of Shigella spp...
February 21, 2017: Proteomics
https://www.readbyqxmd.com/read/28198105/antibiotic-dependent-perturbations-of-extended-spectrum-beta-lactamase-producing-klebsiella-pneumoniae-proteome
#5
Moo-Jin Suh, Sarah L Keasey, Ernst E Brueggemann, Robert G Ulrich
Extended spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KP) causes life-threatening infections in susceptible and immuno-compromised individuals. Because of the emergence of multidrug resistance and tolerance, it is crucial to better understand the mechanisms by which ESBL-KP can adapt to antibiotic stress. The aim of this study was to provide an overview of the global proteome changes occurring in ESBL-KP in response to sub-lethal concentrations of the antibiotics doxycycline (DC, bacteriostatic) and streptomycin (SM, bactericidal), which both impair ribosomal synthesis of bacterial proteins...
February 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28198089/a-comprehensive-proteome-map-of-glandular-trichomes-of-hop-humulus-lupulus-l-female-cones-identification-of-biosynthetic-pathways-of-the-major-terpenoid-related-compounds-and-possible-transport-proteins
#6
Antoine Champagne, Marc Boutry
Female flowers of hop (Humulus lupulus) are an essential source of terpenoid-related compounds, which are mainly used as flavoring in the beer brewing process. The compounds involved are bitter acids, terpenophenolics, as well as mono- and sesquiterpenoids. In this work, we analyzed the proteome of purified glandular trichomes (lupulin glands) from female flowers, which produce and accumulate these compounds. An extensive 2D-LC-MS/MS analysis identified 1,015 proteins. Of these, most correspond to housekeeping and primary metabolism-related proteins, albeit predominantly including amino acid and lipid metabolism, which feeds the specialized (secondary) metabolism...
February 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28195392/relative-protein-quantification-and-accessible-biology-in-lung-tumor-proteomes-from-four-lc-ms-ms-discovery-platforms
#7
Paul A Stewart, Bin Fang, Robbert J C Slebos, Guolin Zhang, Adam L Borne, Katherine Fellows, Jamie K Teer, Y Ann Chen, Eric Welsh, Steven A Eschrich, Eric B Haura, John M Koomen
Discovery proteomics experiments include many options for sample preparation and mass spectrometry data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared 1) single sample liquid chromatography-tandem mass spectrometry (LC-MS/MS) with data dependent acquisition (DDA) to single sample LC-MS/MS with data independent acquisition (DIA) and 2) peptide fractionation with label-free quantification (LF) to isobaric labeling followed by peptide fractionation (TMT 6-plex)...
February 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28191739/itraq-based-quantitative-proteomic-analysis-of-wheat-roots-in-response-to-salt-stress
#8
Qiyan Jiang, Xiaojuan Li, Fengjuan Niu, Xianjun Sun, Zheng Hu, Hui Zhang
Salinity is a major abiotic stress that affects plant growth and development. Plant roots are the sites of salt uptake. Here, an isobaric tag for a relative and absolute quantitation (iTRAQ)-based proteomic technique was employed to identify the differentially expressed proteins (DEPs) from seedling roots of the salt-tolerant genotype Han 12 and the salt-sensitive genotype Jimai 19 in response to salt treatment. A total of 121 NaCl-responsive DEPs were observed in Han 12 and Jimai 19. The main DEPs were ubiquitination-related proteins, transcription factors, pathogen-related proteins, membrane intrinsic protein transporters and antioxidant enzymes, which may work together to obtain cellular homeostasis in roots and determine the overall salt tolerance of different wheat varieties in response to salt stress...
February 13, 2017: Proteomics
https://www.readbyqxmd.com/read/28191734/integrative-proteomics-genomics-and-translational-immunology-approaches-reveal-mutated-forms-of-proteolipid-protein-1-plp1-and-mutant-specific-immune-response-in-multiple-sclerosis
#9
Veneta Qendro, Grace A Bugos, Debbie H Lundgren, John Glynn, May H Han, David K Han
In order to gain mechanistic insights into multiple sclerosis (MS) pathogenesis, we utilized a multi-dimensional approach to test the hypothesis that mutations in myelin proteins lead to immune activation and central nervous system autoimmunity in MS. Mass spectrometry-based proteomic analysis of human MS brain lesions revealed seven unique mutations of PLP1; a key myelin protein that is known to be destroyed in MS. Surprisingly, in-depth genomic analysis of two MS patients at the genomic DNA and mRNA confirmed mutated PLP1 in RNA, but not in the genomic DNA...
February 12, 2017: Proteomics
https://www.readbyqxmd.com/read/28181392/design-of-five-layer-gold-nanoparticles-self-assembled-in-a-liquid-open-tubular-column-for-ultrasensitive-nano-lc-ms-ms-proteomic-analysis-of-80-living-cells
#10
Xi Shao, Xiangmin Zhang
In this work, for the first time, a liquid open tubular column modified by five-layer gold nanoparticles and linked with C18 (GNPs@C18 ) was designed and fabricated for nano-LC-MS/MS analysis of 80 living cells. 60 nm gold nanoparticles were self-assembled layer by layer on the inner wall of a 20-μm-i.d. fused-silica capillary. C18 were then linked on the gold nanoparticles to make the liquid open tubular column show hydrophobic character. Enough loading capacities for analysis of 80 living cells, ∼100 fmol for pk-10 and ∼30 fmol for insulin were obtained with the 2 m × 20-μm-i...
February 8, 2017: Proteomics
https://www.readbyqxmd.com/read/28176486/integrated-analysis-of-proteome-phosphotyrosine-proteome-tyrosine-kinome-and-tyrosine-phosphatome-in-acute-myeloid-leukemia
#11
Jiefei Tong, Mohamed Helmy, Florence M G Cavalli, Lily Jin, Jonathan St-Germain, Robert Karisch, Paul Taylor, Mark D Minden, Michael D Taylor, Benjamin G Neel, Gary D Bader, Michael F Moran
Reversible protein-tyrosine phosphorylation is catalyzed by the antagonistic actions of protein-tyrosine kinases (PTKs) and phosphatases (PTPs), and represents a major form of cell regulation. Acute myeloid leukemia (AML) is an aggressive hematological malignancy that results from the acquisition of multiple genetic alterations, which in some instances are associated with deregulated protein-phosphotyrosine (pY)-mediated signaling networks. However, although individual PTKs and PTPs have been linked to AML and other malignancies, analysis of protein-pY networks as a function of activated PTKs and PTPs has not been done...
February 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28176443/quantitative-phosphoproteomic-analysis-reveals-system-wide-signaling-pathways-regulated-by-site-specific-phosphorylation-on-keratin-8-in-skin-squamous-cell-carcinoma-derived-cell-line
#12
Richa Tiwari, Indrajit Sahu, Bihari Lal Soni, Gajanan J Sathe, Keshava K Datta, Pankaj Thapa, Shruti Sinha, Chella Krishna Vadivel, Bharti Dhaka, Harsha Gowda, Milind M Vaidya
Keratin 8/18, a simple epithelia specific keratin pair, is often aberrantly expressed in squamous cell carcinomas (SCC) where its expression is correlated with increased invasion and poor prognosis. Majority of Keratin 8 (K8) functions are governed by its phosphorylation at Serine(73) (head-domain) and Serine(431) (tail-domain) residues. Although, deregulation of K8 phosphorylation is associated with progression of different carcinomas, its role in skin-SCC and the underlying mechanism is obscure. In this direction, we performed TMT-based quantitative phosphoproteomics by expressing K8 wild type, phosphodead and phosphomimetic mutants in K8-deficient A431 cells...
February 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28165663/interrogating-the-hidden-phosphoproteome
#13
Un-Beom Kang, William M Alexander, Jarrod A Marto
Post-genomic studies continue to highlight the potential clinical importance of protein phosphorylation signaling pathways in drug discovery. Unfortunately the dynamic range and variable stoichiometry of protein phosphorylation continues to stymie efforts to achieve comprehensive characterization of the human phosphoproteome. In this study, we develop a complementary, two-stage method for enrichment of cysteine-containing phosphopeptides combined with TMT multiplex labeling for relative quantification. Use of this approach with multi-dimension fractionation in mammalian cells yielded more than 7,000 unique cys-phosphopeptide sequences, comprising 15%-20% novel phosphorylation sites...
February 6, 2017: Proteomics
https://www.readbyqxmd.com/read/28160437/rapid-synthesis-of-titanium-iv-immobilized-magnetic-mesoporous-silica-nanoparticles-for-endogenous-phosphopeptides-enrichment
#14
Jizong Yao, Nianrong Sun, Jiawen Wang, Yiqin Xie, Chunhui Deng, Xiangmin Zhang
The matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) has already been a main platform for phosphoproteome analysis. However, there are some weaknesses in direct analysis of endogenous phosphopeptides by MALDI-TOF MS because of the serious suppression effect and poor ionization efficiency which is brought by the excess of non-phosphopeptides and protein. It is essential to enrich endogenous phosphopeptides from complex bio-samples efficiently prior to MALDI-TOF MS analysis...
February 4, 2017: Proteomics
https://www.readbyqxmd.com/read/28155257/cell-wall-proteome-analysis-of-arabidopsis-thaliana-mature-stems
#15
Harold Duruflé, Hélène San Clemente, Thierry Balliau, Michel Zivy, Christophe Dunand, Elisabeth Jamet
Plant stems carry flowers necessary for species propagation and need to be adapted to mechanical disturbance and environmental factors. The stem cell walls are different from other organs and can modify their rigidity or viscoelastic properties for the integrity and the robustness required to withstand mechanical impacts and environmental stresses. Plant cell wall is composed of complex polysaccharide networks also containing cell wall proteins (CWPs) crucial to perceive and limit the environmental effects...
February 2, 2017: Proteomics
https://www.readbyqxmd.com/read/28145059/time-space-and-disorder-in-the-expanding-proteome-universe
#16
David-Paul Minde, A Keith Dunker, Kathryn S Lilley
Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (1) alternative sequences, (2) alternative conformations, (3) alternative interactions with a range of biomolecules, (4) cellular localisations, (5) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure...
February 1, 2017: Proteomics
https://www.readbyqxmd.com/read/28133907/discovery-of-gastric-cancer-specific-biomarkers-by-the-application-of-serum-proteomics
#17
Moon-Won Yoo, Jisook Park, Hye-Seung Han, Yeo-Min Yun, Jeong Won Kang, Do-Young Choi, Joon Won Lee, Jae Hun Jung, Kyung-Yung Lee, Kwang Pyo Kim
Current diagnostic markers for gastric cancer are not sufficiently specific or sensitive for use in clinical practice. The aims of this study are to compare the proteomes of serum samples from patients with gastric cancers and normal controls, and to develop useful tumor markers of gastric cancer by quantitative proteomic analysis. We identified a total of 388 proteins with a ≤1% false discovery rate and with at least two unique peptides from the sera of each group. Among them, 215, 251, and 260 proteins were identified in serum samples of patients in an advanced cancer group, early cancer group, and normal control group, respectively...
January 29, 2017: Proteomics
https://www.readbyqxmd.com/read/28130891/dia-is-not-a-new-mass-spectrometry-acquisition-method
#18
Daniel Martins-de-Souza, Vitor M Faça, Fábio C Gozzo
Contrary to what is being said by several colleagues (and even advertised), data independent analysis/acquisition (DIA) is not a new mass spectrometry acquisition method. Here we draw a timeline of events showing that DIA has been around since the early 2000s. This article is protected by copyright. All rights reserved.
January 28, 2017: Proteomics
https://www.readbyqxmd.com/read/28130869/proteomic-analysis-of-human-follicular-fluid-in-poor-ovarian-responders-during-in-vitro-fertilization
#19
Jae Won Oh, Seul Ki Kim, Kyung-Cho Cho, Min-Sik Kim, Chang Suk Suh, Jung Ryeol Lee, Kwang Pyo Kim
Poor ovarian response (POR) observed in controlled ovarian stimulation (COS) is often observed during in vitro fertilization and embryo transfer (IVF-ET) cycles and is a major problem. A POR has been found to be related to several factors, including advanced age, high body mass index, and history of ovarian or pelvic surgery. However, it is difficult to predict POR, as there are no specific biomarkers known. In this study, we used quantitative proteomic analyses to investigate potential biomarkers that can predict poor response during IVF based on follicular fluid samples...
January 28, 2017: Proteomics
https://www.readbyqxmd.com/read/28128880/single-cell-proteomics-in-biomedicine-high-dimensional-data-acquisition-visualization-and-analysis
#20
Yapeng Su, Qihui Shi, Wei Wei
New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data...
January 27, 2017: Proteomics
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