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Proteomics

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https://www.readbyqxmd.com/read/28319648/new-targeted-approaches-for-the-quantification-of-data-independent-acquisition-mass-spectrometry
#1
Roland Bruderer, Julia Sondermann, Chih-Chiang Tsou, Alonso Barrantes-Freer, Christine Stadelmann, Alexey I Nesvizhskii, Manuela Schmidt, Lukas Reiter, David Gomez-Varela
The use of data-independent acquisition (DIA) approaches for the reproducible and precise quantification of complex protein samples has increased in the last years. The protein information arising from DIA analysis is stored in digital protein maps (DIA-maps) that can be interrogated in a targeted way by using ad hoc or publically-available peptide spectral libraries generated on the same sample species as for the generation of the DIA maps. The restricted availability of certain difficult-to-obtain human tissues (i...
March 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28317260/comparative-proteomic-analysis-of-trophoblast-cell-models-reveals-their-differential-phenotypes-potential-uses-and-limitations
#2
Paulina B Szklanna, Kieran Wynne, Marie Nolan, Karl Egan, Fionnuala Ní Áinle, Patricia B Maguire
Trophoblastic cell lines are widely used in in vitro studies of placental function as a surrogate for primary trophoblasts. To date, no reference proteomics dataset exists to directly compare the shared and unique characteristics of these cells. Here, we performed comparative proteomic profiling of the BeWo and HTR8/SVneo cell lines using label-free quantitative mass spectrometry. 1557 proteins were identified, which included 338 uniquely attributed to BeWo cells, and a further 304 specifically identified in HTR8/SVneo cells...
March 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28271636/proximity-labeling-of-interacting-proteins-application-of-bioid-as-a-discovery-tool
#3
REVIEW
Peipei Li, Jingjing Li, Li Wang, Li-Jun Di
Protein performs biochemical functions by forming complexes, or protein-protein interactions (PPIs). Many different approaches, such as phage display and yeast hybridization etc. were developed to illustrate the PPIs, and disclose the composition and organization of protein complexes. However, none of these approaches are based on the real-time and in vivo PPI analysis. Proximity dependent labeling of interacting proteins (PDL) has recently been proposed by taking advantage of several enzymes, which are capable of attaching the known reactive groups to the nearby proteins covalently...
March 8, 2017: Proteomics
https://www.readbyqxmd.com/read/28271630/sample-clean-up-strategies-for-electrospray-ionization-mass-spectrometry-applications-in-bottom-up-proteomics-trends-from-2012-2016
#4
REVIEW
Ria Marni Tubaon, Paul R Haddad, Joselito P Quirino
Bottom-up proteomics is a mass spectrometric (MS)-based approach for the characterization of peptides obtained from in-solution protein digestion. MS is favoured over other methods for peptide and protein analysis because of its better sensitivity and high throughput. Inorganic ions and surfactants present in the sample or produced during tryptic digestion are detrimental in MS analysis and affect the proteome data, thus sample preparation for removal of these unwanted components has become essential. Here, we review 48 research papers on strategies for removal of salts and surfactants (in particular, sodium dodecyl sulfate, SDS) prior to electrospray ionization (ESI)-MS analysis in bottom-up proteomics from 2012-2016...
March 8, 2017: Proteomics
https://www.readbyqxmd.com/read/28267294/comprehensive-proteomic-analysis-of-penicillium-verrucosum
#5
Katharina Nöbauer, Karin Hummel, Corina Mayrhofer, Maike Ahrens, Francis M C Setyabudi, Martin Eisenacher, Ebrahim Razzazi-Fazeli
Mass spectrometric identification of proteins in species lacking validated sequence information is a major problem in veterinary science. In the present study we used ochratoxin A (OTA) producing Penicillium verrucosum to identify and quantitatively analyse proteins of an organism with yet no protein information available. The work presented here aimed to provide a comprehensive protein identification of P. verrucosum using shotgun proteomics. We were able to identify 3631 proteins in an "ab initio" translated database from DNA sequences of P...
March 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28266172/n-glycosylation-proteomic-characterization-and-cross-species-comparison-of-milk-whey-proteins-from-dairy-animals
#6
Yongxin Yang, Nan Zheng, Xiaowei Zhao, Yangdong Zhang, Rongwei Han, Shengguo Zhao, Jinhui Yang, Songli Li, Tongjun Guo, Changjiang Zang, Jiaqi Wang
Glycosylated proteins in milk have been implicated in multiple biological roles. However, the N-glycoprotein components and their complexity in milk whey from dairy animals are not well characterized. Here, a modified proteomics approach consisting of N-glycopeptide enrichment and identification was used to map the N-glycoproteome profile of milk whey from Holstein and Jersey cows, buffaloes, yaks, goats, camels, and horses. A total of 233 N-glycosylation sites, corresponding to 147 N-glycoproteins, were detected in the studied animals...
March 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28266123/evaluation-of-different-peptide-fragmentation-types-and-mass-analyzers-in-data-dependent-methods-using-an-orbitrap-fusion-lumos-tribrid-mass-spectrometer
#7
Guadalupe Espadas, Eva Borràs, Cristina Chiva, Eduard Sabidó
One of the major additions in mass spectrometry technology has been the irruption of the Orbitrap mass analyzer, which has boosted the proteomics analyses of biological complex samples since its introduction. Here, we took advantage of the capabilities of the new Orbitrap Fusion Lumos Tribrid mass spectrometer to assess the performance of different data-dependent acquisition methods for the identification and quantitation of peptides and phosphopeptides in single-shot analysis of human whole cell lysates. Our study explored the capabilities of tri-hibrid mass spectrometers for (phospho-)peptide identification and quantitation using different gradient lengths, sample amounts, and combinations of different peptide fragmentation types and mass analysers...
March 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28256805/targeted-label-free-quantification-of-interleukin-8-in-pma-activated-u937-cell-secretome-by-nanolc-esi-ms-ms-ssrm
#8
Pelin Esma Emirbayer, Kerstin F Gerer, Stefanie Hoyer, Monika Pischetsrieder
Monocytes are a part of the innate immune system. Their differentiation into macrophages changes their cellular proteome and secretome. Particularly secretome components such as cytokines are crucial for immune response and inflammation in many diseases. Differentiation of human lymphoma cell line U937 can be triggered by phorbol 12-myristate 13-acetate (PMA). Screening of the cytokine release in U937 upon PMA stimulation by cytometric bead array almost exclusively showed interleukin-8. Next, a label-free nanoLC-ESI-MS/MS-sSRM method for quantification of interleukin-8 in the cell secretome was established and applied to monitor the time kinetics of PMA treatment in different concentrations...
March 3, 2017: Proteomics
https://www.readbyqxmd.com/read/28252257/quantification-of-small-gtpase-glucosylation-by-clostridial-glucosylating-toxins-using-multiplexed-mrm-analysis
#9
Johannes Junemann, Chantal M Lämmerhirt, Felix Polten, Ingo Just, Ralf Gerhard, Harald Genth, Andreas Pich
Large clostridial toxins (LCT) mono-O-glucosylate small GTPases of the Rho and Ras subfamily. As a result of the glucosylation the GTPases are inhibited and thereby corresponding downstream signaling pathways are disturbed. Current methods for quantifying the extent of glucosylation include sequential [(14) C]glucosylation, sequential [(32) P]ADP-ribosylation and Western Blot detection of non-glucosylated GTPases, with neither method allowing the quantification of the extent of glucosylation of an individual GTPase...
March 2, 2017: Proteomics
https://www.readbyqxmd.com/read/28230319/depletion-of-abundant-human-serum-proteins-by-per-se-imprinted-cryogels-based-on-sample-heterogeneity
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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 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 to 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
#18
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
#19
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
#20
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
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