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Proteomics

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https://www.readbyqxmd.com/read/28409884/altered-protein-expression-pattern-in-colon-tissue-of-mice-upon-supplementation-with-distinct-selenium-compounds
#1
Jette Rahn, Claudia Lennicke, Anna P Kipp, Andreas S Müller, Ludger A Wessjohann, Rudolf Lichtenfels, Barbara Seliger
The essential trace element Selenium (Se) is controversially discussed concerning its role in health and disease. Its various physiological functions are largely mediated by Se incorporation in the catalytic center of selenoproteins. To gain insights into the impact of Se deficiency and of supplementation with different Se compounds (selenite, selenate, selenomethionine) at defined concentrations (recommended, 150 μg/ kg diet; excessive, 750 μg/ kg diet) in murine colon tissues a twenty week feeding experiment was performed followed by analysis of the protein expression pattern of colon tissue specimens by 2D-DIGE and MALDI-TOF MS...
April 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28397356/links-between-critical-proteins-drive-the-controllability-of-protein-interaction-networks
#2
Stefan Wuchty, Toni Boltz, Hande Küçük-McGinty
Focusing on the interactomes of H. sapiens, S. cerevisiae, and E. coli, we investigated interactions between controlling proteins. In particular, we determined critical, intermittent, and redundant proteins based on their tendency to participate in minimum dominating sets (MDSets). Independently of the organisms considered, we found that interactions that involved critical nodes had the most prominent effects on the topology of their corresponding networks. Furthermore, we observed that phosphorylation and regulatory events were considerably enriched when the corresponding transcription factors and kinases were critical proteins, while such interactions were depleted when they were redundant proteins...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28394504/systematic-identification-of-the-protein-substrates-of-udp-galnac-polypeptide-n-acetylgalactosaminyltransferase-t1-t2-t3-using-a-human-proteome-microarray
#3
Zhijue Xu, Xing Li, Shumin Zhou, Wenxian Xie, Jing Wang, Li Cheng, Sheng Wang, Shujuan Guo, Zhaowei Xu, Xin Cao, Menghui Zhang, Biao Yu, Hisashi Narimatsu, Sheng-Ce Tao, Yan Zhang
O-GalNAc glycosylation is the initial step of the mucin-type O-glycosylation. In humans, it is catalyzed by a family of 20 homologous UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts). So far, there is very limited information on their protein substrate specificities. In this study, we developed an on-chip ppGalNAc-Ts assay which could rapidly and systematically identify the protein substrates of each ppGalNAc-T. In detail, we utilized a human proteome microarray as the protein substrates and UDP-GalNAz as the nucleotide sugar donor for click chemistry detection...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28394474/proteomic-identification-of-rainbow-trout-blood-plasma-proteins-and-their-relationship-to-seminal-plasma-proteins
#4
Joanna Nynca, G J Arnold, T Fröhlich, A Ciereszko
The characterization of fish blood proteomes is important for comparative studies of seminal and blood proteins as well as for the analysis of fish immune mechanisms and pathways. In this study LC-MS/MS and 2D DIGE were applied to compare rainbow trout seminal (SP) and blood plasma (BP) proteomes. The 54 differentially abundant proteins identified in SP are involved in a variety of signalling pathways, including protein ubiquitination, liver X receptor/retinoid X receptor (LXR/RXR) and farnesoid X receptor (FXR)/RXR activation, cell cycle and acute phase signalling...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28393466/improving-basic-and-membrane-protein-ms-detection-of-the-culture-filtrate-proteins-from-mycobacterium-tuberculosis-h37rv-by-biomimetic-affinity-pre-fractionation
#5
Guorong Ma, Fuqiang Zhou, Lina Gao, Zhanqiang Sun, Li Deng, Shulin Zhang, Rongxiu Li
The culture filtrate proteins (CFPs) from Mycobacterium tuberculosis (MTB) have been shown to induce protective immune responses in human and animal models, making them a promising source of candidate targets for tuberculosis drugs, vaccines and diagnostics. The constituents of the MTB CFP proteome are complex and vary with growth conditions. To effectively profile CFPs, gel-based pre-fractionation is usually performed before MS analysis. In this study, we describe a novel pre-fractionation approach by which the proteome is divided into seven partially overlapping fractions by biomimetic affinity chromatography (BiAC) using a six-column cascade...
April 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28393464/exo-and-surface-proteomes-of-the-probiotic-bacterium-lactobacillus-acidophilus-ncfm
#6
Hasan Ufuk Celebioglu, Birte Svensson
Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS to find proteins potentially involved in bacteria-host interactions. The exo- and surface proteomes included 43 and 39 different proteins from 72 and 49 successfully identified spots, respectively. Twenty-two proteins were shared between the two proteomes; both contained the major surface layer protein that participates in host interaction as well as several well-known and putative moonlighting proteins...
April 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28390171/class-paired-fuzzy-subnets-a-paired-variant-of-the-rank-based-network-analysis-family-for-feature-selection-based-on-protein-complexes
#7
Wilson Wen Bin Goh, Limsoon Wong
Identifying reproducible yet relevant protein features in proteomics data is a major challenge. Analysis at the level of protein complexes can resolve this issue and we have developed a suite of feature-selection methods collectively referred to as Rank-Based Network Analysis (RBNA). RBNAs differ in their individual statistical test setup but are similar in the sense that they deploy rank-defined weights amongst proteins per sample. This procedure is known as gene fuzzy scoring. Currently, no RBNA exists for paired-sample scenarios where both control and test tissues originate from the same source (e...
April 8, 2017: Proteomics
https://www.readbyqxmd.com/read/28390150/quantitative-proteomics-investigation-of-leaves-from-two-sedum-alfredii-crassulaceae-populations-that-differ-in-cadmium-accumulation
#8
Zhongchun Zhang, Huina Zhou, Qi Yu, Yunxia Li, David G Mendoza-Cózatl, Baosheng Qiu, Pingping Liu, Qiansi Chen
Due to extraordinary their capacity to hypertolerate and hyperaccumulate heavy metals in above-ground tissues, hyperaccumulator species have gained wide attention from researchers seeking biotechnologies to manage environmental heavy metal pollution. However, the molecular basis of hyperaccumulation is still far from being fully understood. Here, we used iTRAQ to perform a quantitative proteomics study of the leaves of Sedum alfredii (Crassulaceae) from hyperaccumulating (HP) and non-hyperaccumulating (NHP) populations...
April 8, 2017: Proteomics
https://www.readbyqxmd.com/read/28390088/functional-dual-hydrophilic-dendrimer-modified-metal-organic-framework-for-the-selective-enrichment-of-n-glycopeptides
#9
Yanan Wang, Jiaxi Wang, Mingxia Gao, Xiangmin Zhang
Analysis of protein glycosylation remains a significant challenge due to the low abundance of glycoproteins or N-glycopeptides. Here we have synthesized an amino-functionalized metal-organic framework (MOF) MIL-101(Cr)-NH2 whose surface is grafted with a hydrophilic dendrimer poly(amidoamine) (PAMAM) for N-glycopeptide enrichment based on the hydrophilic interactions. The selected substrate MOF MIL-101(Cr) owns high surface area which provides nice support for peptide adsorption. In addition, the MOF displayed a good hydrophilic property after being modified with amino groups...
April 8, 2017: Proteomics
https://www.readbyqxmd.com/read/28387473/combining-affinity-enrichment-cross-linking-with-photo-amino-acids-and-mass-spectrometry-for-probing-protein-kinase-d2-interactions
#10
Björn Häupl, Christian H Ihling, Andrea Sinz
We present a novel approach that relies on the affinity capture of protein interaction partners from a complex mixture, followed by covalent fixation via UV-induced activation of incorporated diazirine photo-reactive amino acids (photo-methionine and photo-leucine). The captured protein complexes are enzymatically digested and interacting proteins are identified and quantified by label-free LC/MS analysis. Using HeLa cell lysates with photo-methionine and photo-leucine-labeled proteins, we were able to capture and preserve protein interactions that are otherwise elusive in conventional pull-down experiments...
April 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28387034/swath-id-an-instrument-method-which-combines-identification-and-quantification-in-a-single-analysis
#11
Yang Kang, Lyle Burton, Adam Lau, Stephen Tate
Data-independent acquisition (DIA) approaches, such as SWATH(®) -MS, are showing great potential to reliably quantify significant numbers of peptides and proteins in an unbiased manner. These developments have enhanced interest in developing a single DIA method which integrates qualitative and quantitative analysis, eliminating the need of a pre-built library of peptide spectra which are created through data-dependent acquisition (DDA) methods or from public repositories. Here we introduce a new DIA approach, referred to as "SWATH-ID", which was developed to allow peptide identification as well as quantitation...
April 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28337837/sulfated-hyaluronan-attenuates-inflammatory-signaling-pathways-in-macrophages-involving-induction-of-antioxidants
#12
Florent Jouy, Nadine Lohmann, Elke Wandel, Gloria Ruiz-Gómez, M Teresa Pisabarro, Annette G Beck-Sickinger, Matthias Schnabelrauch, Stephanie Moeller, Jan C Simon, Stefan Kalkhof, Martin von Bergen, Sandra Franz
It is well recognized that high molecular weight hyaluronan (H-HA) exerts potent anti-inflammatory effects while its fragmentation into low molecular weight HA (L-HA) is discussed to promote inflammation. Chemical modification of HA with sulfate groups has been shown to foster its anti-inflammatory activity which seems to be maintained in sulfated low molecular weight HA derivatives (sL-HA). However, the molecular mechanisms by which sL-HA produces its anti-inflammatory activity are not understood. In this study, we used global quantitative proteomics combined with targeted analysis of key proteins to characterize the effect of sL-HA on fully differentiated human inflammatory macrophages (iMФ)...
March 24, 2017: Proteomics
https://www.readbyqxmd.com/read/28319648/new-targeted-approaches-for-the-quantification-of-data-independent-acquisition-mass-spectrometry
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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