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Journal of Proteome Research

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https://www.readbyqxmd.com/read/28102082/characterization-of-the-molecular-mechanisms-underlying-the-chronic-phase-of-stroke-in-a-cynomolgus-monkey-model-of-induced-cerebral-ischemia
#1
Henry C H Law, Samuel S W Szeto, Quan Quan, Yun Zhao, Zaijun Zhang, Olga Krakovska, Leong Ting Lui, Chengyou Zheng, Simon Ming Yuen Lee, K W Michael Siu, Yuqiang Wang, Ivan K Chu
Stroke is one of the main causes of mortality and long-term disability worldwide. The pathophysiological mechanisms underlying this disease are not well understood, particularly in the chronic phase after the initial ischemic episode. In this study, a Macaca fascicularis stroke model consisting of two sample groups, as determined by MRI-quantified infarct volumes as a measure of the stroke severity 28 days after the ischemic episode, was evaluated using qualitative and quantitative proteomics analyses. By using multiple online multidimensional liquid chromatography platforms, 8790 non-redundant proteins that condensed to 5223 protein groups at 1% global false discovery rate (FDR)...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102081/deep-coverage-of-global-protein-expression-and-phosphorylation-in-breast-tumor-cell-lines-using-tmt-10-plex-isobaric-labeling
#2
Fang-Ke Huang, Guoan Zhang, Kevin Lawlor, Arpi Nazarian, John Philip, Paul Tempst, Noah Dephoure, Thomas A Neubert
Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8706 proteins and 28186 phosphopeptides, including 7394 proteins and 23739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102078/on-peptide-selection-for-targeted-protein-quantitation
#3
Cristina Chiva, Eduard Sabidó
Targeted proteomics methods in their different flavors rely on the use of a few peptides as proxies for protein quantitation, which need to be specified either prior or after data acquisition. However, in contrast to discovery methods that use all identified peptides for a given protein to estimate its abundance, targeted proteomics methods are limited in the number of peptides that are used for protein quantitation. As only few peptides per protein are acquired or extracted in targeted experiments, the selection of peptides that are used for targeted protein quantitation becomes crucial...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102076/kinobead-and-single-shot-lc-ms-profiling-identifies-selective-pkd-inhibitors
#4
Martin Golkowski, Rama Subba Rao Vidadala, Chloe K Lombard, Hyong Won Suh, Dustin J Maly, Shao-En Ong
ATP-competitive protein kinase inhibitors are important research tools and therapeutic agents. Because there are >500 human kinases that contain highly conserved active sites, the development of selective inhibitors is extremely challenging. Methods to rapidly and efficiently profile kinase inhibitor targets in cell lysates are urgently needed to discover selective compounds and to elucidate the mechanisms of action for polypharmacological inhibitors. Here, we describe a protocol for microgram-scale chemoproteomic profiling of ATP-competitive kinase inhibitors using kinobeads...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28067522/development-of-a-postcolumn-infused-internal-standard-liquid-chromatography-mass-spectrometry-method-for-quantitative-metabolomics-studies
#5
Hsiao-Wei Liao, Guan-Yuan Chen, Ming-Shiang Wu, Wei-Chih Liao, Ching-Hung Lin, Ching-Hua Kuo
Quantitative metabolomics has become much more important in clinical research in recent years. Individual differences in matrix effects (MEs) and the injection order effect are two major factors that reduce the quantification accuracy in liquid chromatography-electrospray ionization-mass spectrometry-based (LC-ESI-MS) metabolomics studies. This study proposed a postcolumn infused-internal standard (PCI-IS) combined with a matrix normalization factor (MNF) strategy to improve the analytical accuracy of quantitative metabolomics...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28099032/pathogenicity-genes-in-ustilaginoidea-virens-revealed-by-a-predicted-protein-protein-interaction-network
#6
Kang Zhang, Yuejiao Li, Tengjiao Li, Zhi-Gang Li, Tom Hsiang, Ziding Zhang, Wenxian Sun
Rice false smut, caused by Ustilaginoidea virens, produces significant loss in rice yield and grain quality, and has recently emerged as one of the most important rice diseases worldwide. Despite its importance in rice production, relatively few studies have been conducted to illustrate the complex interactome and the pathogenicity gene interactions. Here, a protein-protein interaction (PPI) network of U. virens was built through two well-recognized approaches, interolog and domain-domain interaction-based methods...
January 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28094526/1h-nmr-based-global-metabolic-studies-of-pseudomonas-aeruginosa-upon-exposure-of-the-quorum-sensing-inhibitor-resveratrol
#7
Tongtong Chen, Jiyang Sheng, Yonghong Fu, Ming-Hui Li, Jun-Song Wang, Aiqun Jia
Quorum sensing (QS) is a process of bacterial communication that has been a novel target for drug discovery. Pyocyanin quantification assay confirmed that resveratrol was an effective quorum sensing inhibitor (QSI) against Pseudomonas aeruginosa PAO1. In this study, the global metabolite changes of P. aeruginosa PAO1 exposed to QSI resveratrol were investigated by 1H-NMR spectroscopy. A total of 40 metabolites containing amino acids, organic acid, organic amine and energy storage compounds were identified. The changed metabolic profile indicated that resveratrol influenced pathways including oxidative stress, protein synthesis and energy metabolism...
January 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28067524/urea-artifacts-interfere-with-immuno-purification-of-lysine-acetylation
#8
Ana Martinez-Val, Fernando Garcia, Pilar Ximénez-Embún, Ailyn Martínez Teresa-Calleja, Nuria Ibarz, Isabel Ruppen, Javier Munoz
Comprehensive analysis of post-translational modifications (PTMs) often depends on the purification of modified peptides prior to LC-MS/MS. The implementation of these enrichment methods requires thorough knowledge of the experimental conditions to achieve optimal selectivity and sensitivity. In this regard, large-scale analysis of lysine acetylation, a key PTM for multiple cellular processes, makes use of monoclonal pan-antibodies designed against this moiety. We report that the immuno-purification of lysine-acetylated peptides is hampered by the copurification of lysine carbamylated peptides, a frequent urea artifact...
January 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28092160/discovery-of-metabolite-biomarkers-for-acute-ischemic-stroke-progression
#9
Peifang Liu, Ruiting Li, Anton A Antonov, Lihua Wang, Wei Li, Yunfei Hua, Huimin Guo, Lijuan Wang, Peijia Liu, Lixia Chen, Yuan Tian, Fengguo Xu, Zunjian Zhang, Yulan Zhu, Yin Huang
Stroke remains a major public health problem worldwide; it causes severe disability and is associated with high mortality rates. However, early diagnosis of stroke is difficult, and no reliable biomarkers are currently established. In this study, mass spectrometry-based metabolomics was utilized to characterize the metabolic features of the serum of patients with acute ischemic stroke (AIS) to identify novel sensitive biomarkers for diagnosis and progression. First, global metabolic profiling was performed on a training set of 80 human serum samples (40 cases and 40 controls)...
January 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28088865/mass-spectrometry-of-intact-proteins-reveals-98-u-chemical-artefacts-following-precipitation-in-acetone
#10
Melda Zeynep Güray, Shi Zheng, Alan Austin Doucette
Protein precipitation in acetone is frequently employed ahead of mass spectrometry for sample preconcentration and purification. Unfortunately, acetone is not chemically inert; mass artefacts have previously been observed on glycine-containing peptides when exposed to acetone under acidic conditions. We herein report a distinct chemical modification occurring at the level of intact proteins when incubated in acetone. This artefact manifests as one or more satellite peaks in the MS spectrum of intact protein, spaced 98 u above the mass of the unmodified protein...
January 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28088864/an-integrated-high-throughput-multi-omics-platform-enables-data-driven-construction-of-cellular-responses-and-reveals-global-drug-mechanisms-of-action
#11
Jeremy L Norris, Melissa A Farrow, Danielle B Gutierrez, Lauren D Palmer, Nicole Muszynski, Stacy D Sherrod, James C Pino, Jamie L Allen, Jeffrey M Spraggins, Alex L R Lubbock, Ashley T Jordan, William Burns, James C Poland, Carrie E Romer, M Lisa Manier, Yuan-Wei Nei, Boone M Prentice, Kristie L Rose, Salisha Hill, Raf Van de Plas, Tina Tsui, Nathaniel M Braman, M Ray Keller, Stacey A Rutherford, Nichole A Lobdell, Carlos F Lopez, D Borden Lacy, John A McLean, John Peter Wikswo, Eric P Skaar, Richard M Caprioli
An understanding of how cells respond to perturbation is essential for biological applications; however, most approaches for profiling cellular response are limited in scope to pre-established targets. Global analysis of molecular mechanism will advance our understanding of the complex networks constituting cellular perturbation and lead to advancements in areas, such as infectious disease pathogenesis, developmental biology, pathophysiology, pharmacology, and toxicology. We have developed a high-throughput multi-omics platform for comprehensive, de novo characterization of cellular mechanisms of action...
January 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28076955/post-translational-modifications-of-trypanosoma-cruzi-canonical-and-variant-histones
#12
Gisele F A Picchi, Vanessa Zulkievicz, Marco Aurelio Krieger, Nilson T Zanchin, Samuel Goldenberg, Lyris M F de Godoy
Chagas disease, caused by Trypanosoma cruzi, still affects millions of people around the world. No vaccines neither treatment for chronic Chagas disease are available, and chemotherapy for the acute phase is hindered by limited efficacy and severe side effects. The processes by which the parasite acquires infectivity and survives in different hosts involve tight regulation of gene expression, mainly post-transcriptionally. Nevertheless, chromatin structure/organization of trypanosomatids is similar to other eukaryotes, including histone variants and post-translational modifications...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28076954/identification-of-genes-associated-with-breast-cancer-metastasis-to-bone-on-a-protein-protein-interaction-network-with-a-shortest-path-algorithm
#13
Yu-Dong Cai, Qing Zhang, Yu-Hang Zhang, Lei Chen, Tao Huang
Tumor metastasis is defined as the spread of tumor cells from one organ or part to another that is not directly connected to it, which significantly contributes to the progression and aggravation of tumorigenesis. Because it always involves multiple organs, the metastatic process is difficult to study in its entirety. Complete identification of the genes related to this process is an alternative way to study metastasis. In this study, we developed a computational method to identify such genes. To test our method, we selected breast cancer bone metastasis...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28076950/single-amino-acid-variant-profiles-of-subpopulations-in-the-mcf-7-breast-cancer-cell-line
#14
Zhijing Tan, Song Nie, Sean P McDermott, Max S Wicha, David M Lubman
Cancers are initiated and developed from a small population of stem-like cells termed cancer stem cells (CSCs). There is heterogeneity among this CSC population that leads to multiple subpopulations with their own distinct biological features and protein expression. The protein expression and function may be impacted by amino acid variants that can occur largely due to single nucleotide changes. We have thus performed proteomic analysis of breast CSC subpopulations by mass spectrometry to study the presence of single amino acid variants (SAAVs) and their relation to breast cancer...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28075131/classical-galactosemia-insight-into-molecular-pathomechanisms-by-differential-membrane-proteomics-of-fibroblasts-under-galactose-stress
#15
Simon Staubach, Stefan Müller, Murat Pekmez, Franz-Georg Hanisch
Classical galactosemia, a hereditary metabolic disease caused by the deficiency of galactose-1-phosphate uridyltransferase (GALT; EC 2.7.712), results in an impaired galactose metabolism and serious long-term developmental affection of the CNS and ovaries, potentially related in part to endogenous galactose-induced protein dysglycosylation. In search for galactose-induced changes in membrane raft proteomes of GALT-deficient cells, we performed differential analyses of lipid rafts from patient-derived (Q) and sex- and age-matched control fibroblasts (H) in the presence or absence of the stressor...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28051317/argc-like-digestion-complementary-or-alternative-to-tryptic-digestion
#16
Vahid Golghalyani, Moritz Neupärtl, Ilka Wittig, Ute Bahr, Michael Karas
Enzymatic digestion of complex protein samples is often performed by use of multiple proteases to improve protein identification and characterization. Combining trypsin with ArgC is one option to enhance sequence coverage in bottom-up proteomics. However, the low selectivity of this endoprotease derogates from the benefit of the combination. Our approach here is to mimic ArgC digestion by chemically modifying all lysine residues in proteins so that trypsin can only cleave C-terminal to arginine. Four different amine modifications, dimethylation, acetylation, propionylation, and carbethoxylation, were tested, and the protocols were optimized...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28034318/sensitive-and-precise-characterization-of-combinatorial-histone-modifications-by-selective-derivatization-coupled-with-rplc-ethcd-ms-ms
#17
Rijing Liao, Dan Zheng, Aiying Nie, Shaolian Zhou, Haibing Deng, Yuan Gao, Pengyuan Yang, Yanyan Yu, Lin Tan, Wei Qi, Jiaxi Wu, En Li, Wei Yi
Deciphering the combinatorial histone codes has been a long-standing interest in the epigenetics field, which requires the reliable and robust characterization of the post-translational modifications (PTMs) coexisting on histones. To this end, weak cation exchange hydrophilic interaction liquid chromatography is commonly used in middle-down liquid chromatography-mass spectrometry approaches for online separation of variously modified histone peptides. Here we provide a novel strategy that combines the selective histone peptide derivatization using N-hydroxysuccinimide propionate ester with reversed-phase liquid chromatography (RPLC) for the robust, sensitive, and reliable characterization of combinatorial histone PTMs...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/27936760/system-wide-quantitative-proteomics-of-the-metabolic-syndrome-in-mice-genotypic-and-dietary-effects
#18
Camille Terfve, Eduard Sabidó, Yibo Wu, Emanuel Gonçalves, Meena Choi, Stefania Vaga, Olga Vitek, Julio Saez-Rodriguez, Ruedi Aebersold
Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a part in the onset of the metabolic syndrome, its molecular basis and dependency on dietary and genotypic factors are poorly characterized. Here, we used an experimental design with two different mouse strains and dietary and metabolic perturbations to generate a compendium of quantitative proteome data using three mass spectrometric techniques...
January 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28067528/urinary-1-h-nmr-metabolomic-fingerprinting-reveals-biomarkers-of-pulse-consumption-related-to-energy-metabolism-modulation-in-a-subcohort-from-the-predimed-study
#19
Francisco Madrid-Gambin, Rafael Llorach, Rosa Vázquez-Fresno, Mireia Urpi-Sarda, Enrique Almanza-Aguilera, Mar Garcia-Aloy, Ramón Estruch, Dolores Corella, Cristina Andres-Lacueva
Little is known about the metabolome fingerprint of pulse consumption. The study of robust and accurate biomarkers for pulse dietary assessment has great value for nutritional epidemiology regarding health benefits and their mechanisms. To characterize the fingerprinting of dietary pulses (chickpeas, lentils and beans), spot urine samples from a subcohort from the PREDIMED study were stratified, using a validated food frequency questionnaire. Non-pulse consumers (≤ 4 g/day of pulse intake) and habitual pulse consumers (≥ 25 g/day of pulse intake) were analysed using a 1H-NMR metabolomics approach combined with multi- and univariate data analysis...
January 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28067053/global-profiling-of-metabolite-and-lipid-soluble-microbial-products-in-anaerobic-wastewater-reactor-supernatant-using-uplc-mse
#20
Phornpimon Tipthara, Chinagarn Kunacheva, Yan Ni Annie Soh, Stephen C C Wong, Ng Sean Pin, David C Stuckey, Bernhard O Boehm
Identification of soluble microbial products (SMPs) released during bacterial metabolism in mixed cultures in bioreactors is essential to understanding fundamental mechanisms of their biological production. SMPs constitute one of the main foulants (together with colloids and bacterial flocs) in membrane bioreactors widely used to treat, and ultimately recycle wastewater. More importantly, the composition and origin of potentially toxic, carcinogenic, or mutagenic SMPs in renewable/reused water supplies must be determined and controlled...
January 9, 2017: Journal of Proteome Research
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