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Journal of Proteome Research

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https://www.readbyqxmd.com/read/28525284/intrinsically-disordered-proteins-as-important-players-during-desiccation-stress-of-the-soybean-radicles
#1
Yun Liu, Jiahui Wu, Nan Sun, Chengjian Tu, Xiaoying Shi, Hua Cheng, Simu Liu, Shuiming Li, Yong Wang, Yizhi Zheng, Vladimir N Uversky
Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100°C for 10 min) was present in R0mm and R15mm radicles (i.e., before the radicle emergence and the 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%)...
May 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28517934/plasma-and-serum-metabolite-association-networks-comparability-within-and-between-studies-using-nmr-and-ms-profiling
#2
Maria Suarez-Diez, Jonathan Adam, Jerzy Adamski, Styliani A Chasapi, Claudio Luchinat, Annette Peters, Cornelia Prehn, Claudio Santucci, Alexandros Spyridonidis, Georgios A Spyroulias, Leonardo Tenori, Rui Wang-Sattler, Edoardo Saccenti
Blood is one of the most used biofluids in metabolomics studies and the serum and plasma fractions are routinely used as a proxy for blood itself. Here, we investigated the associations networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ~1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA-MS/MS...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28516784/in-culture-cross-linking-of-bacterial-cells-reveals-large-scale-dynamic-protein-protein-interactions-at-the-peptide-level
#3
Luitzen de Jong, Edward A de Koning, Winfried Roseboom, Hansuk Buncherd, Martin J Wanner, Irena Dapic, Petra J Jansen, Jan H van Maarseveen, Garry L Corthals, Peter J Lewis, Leendert Willem Hamoen, Chris G de Koster
Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28516782/exploring-site-specific-n-glycosylation-of-hek293-and-plant-produced-human-iga-isotypes
#4
Kathrin Göritzer, Daniel Maresch, Friedrich Altmann, Christian Obinger, Richard Strasser
The full potential of recombinant Immunoglobulin A as therapeutic antibody is not fully explored, owing to the fact that structure-function relationships of these extensively glycosylated proteins are not well understood. Here, monomeric IgA1, IgA2m(1) and IgA2m(2) variants of the anti-HER2 antibody (IgG1) trastuzumab were expressed in glyco-engineered Nicotiana benthamiana plants and in human HEK293-6E cells. All three IgA isotypes were purified and subjected to biophysical and biochemical characterization...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28516777/improvements-in-mass-spectrometry-assay-library-generation-for-targeted-proteomics
#5
Johan Teleman, Simon Hauri, Johan Malmström
In data independent acquisition mass spectrometry (DIA-MS), targeted extraction of peptide signals in silico using mass spectrometry assay libraries is a successful method for the identification and quantification of proteins. Still, it remains unclear if high quality assay libraries with more accurate peptide ion coordinates can improve peptide target identification rates in DIA analysis. In this study, we systematically improved and evaluated the common algorithmic steps for assay library generation and demonstrate that increased assay quality results in substantially higher identification rates of peptide targets from mouse organ protein lysates measured by DIA-MS...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28516774/multiplexed-mrm-based-protein-quantitation-using-two-different-stable-isotope-labeled-peptides-for-calibration
#6
André LeBlanc, Sarah A Michaud, Andrew J Percy, Darryl B Hardie, Juncong Yang, Nicholas J Sinclair, Jillaine I Proudfoot, Adam Pistawka, Derek S Smith, Christoph H Borchers
Precise and robust quantitation of the endogenous plasma proteome is a requirement for fundamental and biomedical research as well as for clinical applications. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope labeled peptides. However, when measuring protein in plasma, the unknown endogenous levels prevent the implementation of best calibration strategies since no blank matrix is available...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28506058/differential-protein-analysis-of-ipec-j2-cells-infected-with-porcine-epidemic-diarrhea-virus-pandemic-and-classical-strains-elucidates-the-pathogenesis-of-infection
#7
Huixing Lin, Bin Li, Lei Chen, Zhe Ma, Kongwang He, Hongjie Fan
Porcine epidemic diarrhea (PED) re-emerged in China in late 2010 and has now become widespread. Accumulated evidence indicates that this large-scale outbreak of diarrhea was caused by variants of the highly virulent porcine epidemic diarrhea virus (PEDV). A pandemic PEDV YC2014 strain (YC2014) was isolated from clinical samples. An iTRAQ-based comparative quantitative proteomic study of IPEC-J2 cells infected with YC2014 and a classical CV777 strain (CV777) was performed to determine the differences between pandemic and classical PEDV strain infection...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28492082/metabolomics-approach-in-the-investigation-of-metabolic-changes-in-obese-men-after-24-weeks-of-combined-training
#8
Renata G Duft, Alex Castro, Ivan L P Bonfante, Diego T Brunelli, Mara P T Chacon-Mikahil, Cláudia R Cavaglieri
Obesity is associated with comorbidities related to metabolic disorders due to excess of adipose tissue. Physical exercise has a major role in the prevention of obesity. Combined training (CT), in particular, has been shown to improve markers of health. In this study, we used (1)H NMR-based metabolomics to investigate changes in the metabolism of obese men after 24 weeks of CT. Twenty-two obese (body mass index 31 ± 1.4 kg/m(2)), middle-aged men (48.2 ± 6.1 years) were randomly assigned to a control group (CG, n = 11) or CT group (n = 11)...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28514846/natural-mutagenesis-enabled-global-proteomic-study-of-metabolic-and-carbon-source-implications-in-mutant-thermoacidophillic-archaeon-sulfolobus-solfataricus-pbl2025
#9
Wen Qiu, Trong Khoa Pham, Xin Zou, Saw Yen Ow, Phillip C Wright
The thermoacidophilic crenarchaeon Sulfolobus solfataricus has been widely used as a model organism for archaeal systems biology research. Investigation using its spontaneous mutant PBL2025 provides an effective metabolic baseline to study subsequent mutagenesis-induced process shifts as well as changes in feedback inhibitions. Here, an untargeted metabolic investigation using quantitative proteomics and metabolomics was performed to correlate changes in S. solfataricus strains P2 against PBL2025 and under both glucose and tryptone...
May 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28488443/itraq-and-rna-seq-analyses-provide-new-insights-into-regulation-mechanism-of-symbiotic-germination-of-dendrobium-officinale-seeds-orchidaceae
#10
Juan Chen, Si Si Liu, Annegret Kohler, Bo Yan, Hong Mei Luo, Xiao Mei Chen, Shun Xing Guo
Mycorrhizal fungi colonize orchid seeds and induce germination. This so-called symbiotic germination is a critical developmental process in the lifecycle of all orchid species. However, the molecular changes that occur during orchid seed symbiotic germination remain largely unknown. To better understand the molecular mechanism of orchid seed germination, we performed a comparative transcriptomic and proteomic analysis of the Chinese traditional medicinal orchid Dendrobium officinale to explore the change in protein expression at the different developmental stages during asymbiotic and symbiotic germination and identify the key proteins that regulate the symbiotic germination of orchid seeds...
May 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28509555/differential-phosphoproteomic-analysis-of-recombinant-chinese-hamster-ovary-cells-following-temperature-shift
#11
Michael Henry, Martin Power, Prashant Kaushik, Orla Coleman, Martin Clynes, Paula Meleady
Phosphorylation is one of the most important post-translational modifications, playing a crucial role in regulating many cellular processes including transcription, cytoskeletal rearrangement, cell proliferation, differentiation, apoptosis and signal transduction. However, to date little work has been carried out on the phosphoproteome in CHO cells. In this study we have carried out a large scale differential phosphoproteomic analysis of recombinant CHO cells following a reduction of culture temperature (temperature shift)...
May 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28508642/identification-of-alternative-splice-variants-using-unique-tryptic-peptide-sequences-for-database-searches
#12
Trung The Tran, Ravi Chand Bollineni, Margarita Strozynski, Christian J Koehler, Bernd Thiede
Alternative splicing is a mechanism in eukaryotes by which different forms of messenger RNAs (mRNAs) are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database which contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant specific peptide sequences that match to MS data...
May 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28503925/proteomics-provides-insight-into-the-interaction-between-mulberry-and-silkworm
#13
Dandan Wang, Zhaoming Dong, Yan Zhang, Kaiyu Guo, Pengchao Guo, Ping Zhao, Qingyou Xia
Mulberry leaves have been selected as food source for the silkworm (Bombyx mori) over 5000 years. However, the interaction mechanisms of mulberry-silkworm remain largely unknown. In this study, we try to explore the interaction between mulberry and silkworm at the protein level. Total proteins were extracted from mulberry leaves and silkworm feces on day 5 of the fifth larval instar, and analyzed on shotgun liquid chromatography-tandem mass spectrometry, respectively. In total, 2076 and 210 foliar proteins were identified from mulberry leaves and silkworm feces, respectively...
May 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28485144/hydrophobic-interaction-chromatography-for-bottom-up-proteomics-analysis-of-single-proteins-and-protein-complexes
#14
Michal Rackiewicz, Ludger Große-Hovest, Andrew J Alpert, Mostafa Zarei, Jörn Dengjel
Hydrophobic interaction chromatography (HIC) is a robust standard analytical method to purify proteins while preserving their biological activity. It is widely used to study post-translational modifications of proteins and drug-protein interactions. In the current manuscript we employed HIC to separate proteins, followed by bottom-up LC-MS/MS experiments. We used this approach to fractionate antibody species followed by comprehensive peptide mapping as well as to study protein complexes in human cells. HIC-reversed-phase chromatography (RPC)-mass spectrometry (MS) is a powerful alternative to fractionate proteins for bottom-up proteomics experiments making use of their distinct hydrophobic properties...
May 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28480704/unbiased-protein-association-study-on-the-public-human-proteome-reveals-biological-connections-between-co-occurring-protein-pairs
#15
Surya Gupta, Kenneth Verheggen, Jan Tavernier, Lennart Martens
Mass-spectrometry-based, high-throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be reused in orthogonal ways to reveal new biological knowledge. We here present a novel method for such orthogonal data reuse of public proteomics data. Our method elucidates biological relationships between proteins based on the co-occurrence of these proteins across human experiments in the PRIDE database. The majority of the significantly co-occurring protein pairs that were detected by our method have been successfully mapped to existing biological knowledge...
May 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28474894/thermal-shock-induces-host-proteostasis-disruption-and-endoplasmic-reticulum-stress-in-the-model-symbiotic-cnidarian-aiptasia
#16
Clinton A Oakley, Elysanne Durand, Shaun P Wilkinson, Lifeng Peng, Virginia M Weis, Arthur R Grossman, Simon K Davy
Coral bleaching has devastating effects on coral survival and reef ecosystem function, but many of the fundamental cellular effects of thermal stress on cnidarian physiology are unclear. We used label-free liquid chromatography-tandem mass spectrometry to compare the effects of rapidly (33.5 °C, 24 h) and gradually (30 and 33.5 °C, 12 days) elevated temperatures on the proteome of the model symbiotic anemone Aiptasia. We identified 2133 proteins in Aiptasia, 136 of which were differentially abundant between treatments...
May 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28467092/metabolomics-proteomics-combined-approach-identifies-differential-metabolism-associated-molecular-events-between-senescence-and-apoptosis
#17
Mengqiu Wu, Hui Ye, Chang Shao, Xiao Zheng, Qingran Li, Lin Wang, Min Zhao, Gaoyuan Lu, Baoqiang Chen, Jun Zhang, Yun Wang, Guangji Wang, Haiping Hao
Apoptosis and senescence are two types of cell fates in response to chemotherapy. Besides canonical pathways that mediate cell fates, cancer cell metabolism has been revealed as a crucial factor affecting cell fate decisions and thus represents a new target for antitumor therapy. Therefore, a comprehensive description of metabolic pathways underlying cell senescence and apoptosis in response to chemotherapy is highly demanded for therapeutic exploitation of both processes. Herein we employed a metabolomics-proteomics combined approach to identify metabolism-associated molecular events that mediate cellular responses to senescence and apoptosis using doxorubicin-treated human breast cancer cells MCF7 as models...
May 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28452488/metabolomics-study-of-the-effects-of-inflammation-hypoxia-and-high-glucose-on-isolated-human-pancreatic-islets
#18
Marta Garcia-Contreras, Alejandro Tamayo-Garcia, Kirk L Pappan, Gregory A Michelotti, Cherie L Stabler, Camillo Ricordi, Peter Buchwald
The transplantation of human pancreatic islets is a therapeutic possibility for a subset of type 1 diabetic patients who experience severe hypoglycemia. Pre- and post-transplantation loss in islet viability and function, however, is a major efficacy-limiting impediment. To investigate the effects of inflammation and hypoxia, the main obstacles hampering the survival and function of isolated, cultured, and transplanted islets, we conducted a comprehensive metabolomics evaluation of human islets in parallel with dynamic glucose-stimulated insulin release (GSIR) perifusion studies for functional evaluation...
May 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28481548/cross-sectional-association-of-salivary-proteins-with-age-sex-body-mass-index-smoking-and-education
#19
Annette Murr, Christiane Pink, Elke Hammer, Stephan Michalik, Vishnu Mukund Dhople, Birte Holtfreter, Uwe Völker, Thomas Kocher, Manuela Gesell Salazar
Whole saliva is gaining more and more attention as a diagnostic tool to study disease-specific changes in human subjects. Prior to the actual disease-related analyses, it is important to understand the influence of various demographic variables and coupled phenotypes on salivary protein signatures. In a cross-sectional approach, we analyzed the influence of age, sex, body mass index (BMI), smoking, and education on salivary protein signatures in whole saliva samples of 187 individuals. Subjects were randomly selected from the population-based Study of Health in Pomerania (SHIP-Trend)...
May 8, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28452485/systematic-comparison-of-false-discovery-rate-controlling-strategies-for-proteogenomic-search-using-spike-in-experiments
#20
Honglan Li, Jonghun Park, Hyunwoo Kim, Kyu-Baek Hwang, Eunok Paek
Proteogenomic searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated, however, mainly due to the difficulty in confirming the existence of identified novel peptides. We simulated a proteogenomic search using a controlled, spike-in proteomic data set. After confirming that the results of the simulated proteogenomic search were similar to those of a real proteogenomic search using a human cell line data set, we evaluated the performance of six FDR control methods-global, separate, and multistage FDR estimation, respectively, coupled to a target-decoy search and a mixture model-based method-on novel peptide identification...
May 5, 2017: Journal of Proteome Research
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