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Journal of Proteome Research

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https://www.readbyqxmd.com/read/29790754/epiprofile-2-0-a-computational-platform-for-processing-epi-proteomics-mass-spectrometry-data
#1
Zuo-Fei Yuan, Simone Sidoli, Dylan M Marchione, Johayra Simithy, Kevin A Janssen, Mary R Szurgot, Benjamin A Garcia
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here, we present EpiProfile 2.0, an extended version of our 2015 software (v1.0) for accurate quantification of histone peptides based on liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29790753/target-decoy-based-false-discovery-rate-estimation-for-large-scale-metabolite-identification
#2
Xusheng Wang, Drew R Jones, Timothy I Shaw, Ji-Hoon Cho, Yuanyuan Wang, Haiyan Tan, Boer Xie, Suiping Zhou, Yuxin Li, Junmin Peng
Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. In this study, we report a novel method for estimating false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis, and was also evaluated with two other metabolomics tools, mzMatch and mzMine 2...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29790350/glutaredoxin-deletion-shortens-chronological-life-span-in-saccharomyces-cerevisiae-via-ros-mediated-ras-pka-activation
#3
Yan Liu, Fan Yang, Siying Li, Junbiao Dai, Haiteng Deng
Glutaredoxins (GRXs), small redox proteins that use reduced glutathione (GSH) as an electron donor, are key components of the cellular antioxidant system. In this study, we used Saccharomyces cerevisiae as a model system to investigate the effects of GRX deletion on yeast chronological life span (CLS). Deletion of either Grx1 or Grx2 shortened yeast CLS. Quantitative proteomics revealed that GRX deletion decreased expression of stress-response proteins, leading to increased cellular reactive oxygen species (ROS) accumulation and, subsequently, intracellular acidification...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29775069/simultaneous-release-and-labelling-of-o-and-n-glycans-allowing-for-rapid-glycomic-analysis-by-online-lc-uv-esi-ms-ms
#4
Chengjian Wang, Yu Lu, Jianli Han, Wanjun Jin, Lingmei Li, Ying Zhang, Xuezheng Song, Linjuan Huang, Zhongfu Wang
Most glycoproteins and biological protein samples undergo both O- and N-glycosylation, making characterization of their structures very complicated and time-consuming. Nevertheless, to fully understand the biological functions of glycosylation, both the glycosylation forms need to be analyzed. Herein we report a versatile, convenient one-pot method in which O- and N-glycans are simultaneously released from glycoproteins and chromogenically labelled in situ and thus available for further characterization. In this procedure, glycoproteins are incubated with 1-phenyl-3-methyl-5-pyrazolone (PMP) in aqueous ammonium hydroxide, making O-glycans released from protein backbones by beta-elimination and N-glycans liberated by alkaline hydrolysis...
May 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29775065/maldi-imaging-analysis-of-neuropeptides-in-africanized-honeybee-apis-mellifera-brain-effect-of-aggressiveness
#5
Marcel Pratavieira, Anally Ribeiro da Silva Menegasso, Franciele Grego Esteves, Kenny Umino Sato, Osmar Malaspina, Mario Sérgio Palma
The aggressiveness in honeybees seems to be regulated by multiple genes, under the influence of different factors, such as polyethism of workers, environmental factors, and response to alarm pheromones, creating a series of behavioral responses. It is suspected that neuropeptides seem to be involved with the regulation of the aggressive behavior. The role of allatostatin and tachykinin-related neuropeptides in honeybee brain during the aggressive behavior is unknown; thus, worker honeybees were stimulated to attack and to sting leather targets hanged in front of the colonies...
May 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29774740/searchgui-a-highly-adaptable-common-interface-for-proteomics-search-and-de-novo-engines
#6
Harald Barsnes, Marc Vaudel
Mass spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences, for later mapping to the originating proteins. We here present the latest developments to SearchGUI, a common open source interface for the most frequently used freely available proteomics search and de novo engines, which has evolved into a central component in numerous bioinformatics workflows...
May 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29770699/lysine-succinylation-and-acetylation-in-pseudomonas-aeruginosa
#7
Charlotte Gaviard, Isabelle Broutin, Pascal Cosette, Emmanuelle De, Thierry Jouenne, Julie Hardouin
Pseudomonas aeruginosa is a Multi-Drug Resistant human opportunistic pathogen largely involved in nosocomial infections. Unfortunately, effective antibacterial agents lacked. Explore its physiology at the post-translational modifications (PTMs) level may contribute to the renewal of combat tactics. Recently, lysine succinylation was discovered in bacteria and seems to be an interesting PTM. Here, we present the first succinylome and acetylome of P. aeruginosa PA14 cultured in the presence of 4 different carbon sources, using a two-dimensional immunoaffinity approach coupled with nano-liquid chromatograpy tandem mass spectrometry...
May 17, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29766714/the-outer-membrane-vesicle-proteome-of-porphyromonas-gingivalis-is-differentially-modulated-relative-to-the-outer-membrane-in-response-to-heme-availability
#8
Paul D Veith, Caroline Luong, Keng H Tan, Stuart G Dashper, Eric C Reynolds
Porphyromonas gingivalis is an anaerobic, Gram-negative oral pathogen associated with chronic periodontitis. P. gingivalis has an obligate requirement for heme which it obtains from the host. Heme availability has been linked to disease initiation and progression. In this study we used continuous culture of the bacterium to determine the effect of heme limitation and excess on the P. gingivalis proteome. Four biological replicates of whole cell lysate (WCL) and outer membrane vesicle (OMV) samples were digested with trypsin and analysed by tandem mass spectrometry and MaxQuant label-free quantification...
May 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29734811/streamlined-tandem-mass-tag-sl-tmt-protocol-an-efficient-strategy-for-quantitative-phospho-proteome-profiling-using-tandem-mass-tag-synchronous-precursor-selection-ms3
#9
José Navarrete-Perea, Qing Yu, Steven P Gygi, Joao A Paulo
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol...
May 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29762036/biochemical-profiling-of-the-brain-and-blood-metabolome-in-a-mouse-model-of-prodromal-parkinson-s-disease-reveal-distinct-metabolic-profiles
#10
Stewart F Graham, Nowlen L Rey, Ali Yilmaz, Praveen Kumar, Zachary Madaj, Michael Maddens, Ray O Bahado-Singh, Katelyn Becker, Emily Schulz, Lindsay K Meyerdirk, Jennifer A Steiner, Jiyan Ma, Patrik Brundin
Parkinson's disease is the second most common neurodegenerative disease. In the vast majority of cases the origin is not genetic and the cause is not well understood, although progressive accumulation of α-synuclein aggregates appears central to the pathogenesis. Currently, treatments that slow disease progression are lacking and there are no robust biomarkers that can facilitate development of such treatments, or act as aids in early diagnosis. Therefore, we have defined metabolomic changes in the brain and serum in an animal model of prodromal Parkinson's disease...
May 15, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29761697/identification-of-proteins-using-itraq-and-vigs-reveals-three-bread-wheat-proteins-involved-in-the-response-to-combined-osmotic-cold-stress
#11
Ning Zhang, Lingran Zhang, Chaonan Shi, Lei Zhao, Dangqun Cui, Feng Chen
Crops are often subjected to a combination of stresses in the field. To date, studies on the physiological and molecular responses of common wheat to a combination of osmotic and cold stresses, however, remain unknown. In this study, wheat seedlings exposed to osmotic-cold stress for 24 h showed inhibited growth, as well as increased lipid peroxidation, relative electrolyte leakage, and soluble sugar contents. iTRAQ-based quantitative proteomics and liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods were employed to determine the proteomic profiles of the roots and leaves of wheat seedlings exposed to osmotic-cold stress conditions...
May 15, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29757649/functional-annotation-of-proteins-encoded-by-the-minimal-bacterial-genome-based-on-secondary-structure-element-alignment
#12
Zhiyuan Yang, Stephen Kwok-Wing Tsui
In synthetic biology, one of key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0, which only encoded 438 essential proteins. However, among them functions of 149 proteins remain unknown because of the lack of effective annotation method. Here, we report a secondary structure element alignment method called SSEalign based on an effective training dataset extracting from various bacterial genomes...
May 14, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29754492/comparison-of-in-solution-fasp-and-s-trap-based-digestion-methods-for-bottom-up-proteomic-studies
#13
Katelyn R Ludwig, Monica M Schroll, Amanda B Hummon
Bottom-up proteomic strategies rely on efficient digestion of proteins into peptides for mass spectrometry analysis. In-solution and filter-based strategies are commonly used for proteomic analysis. In recent years, filter-aided sample preparation (FASP) has become the dominant filter-based method due to its ability to remove SDS prior to mass spectrometry analysis. However, the time-consuming nature of FASP protocols have led to the development of new filter-based strategies. Suspension traps (S-Traps) were recently reported as an alternative to FASP and in-solution strategies as they allow for high concentrations of SDS in a fraction of the time of a typical FASP protocol...
May 13, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29750532/proteomic-analysis-and-nir-ii-imaging-of-mcm2-protein-in-hepatocellular-carcinoma
#14
Jing Yang, Qi Xie, Hui Zhou, Lei Chang, Wei Wei, Yin Wang, Hong Li, Zixin Deng, Yuling Xiao, Junzhu Wu, Ping Xu, Xuechuan Hong
Targeted therapy of hepatocellular carcinoma (HCC) is essential for improved therapies. Therefore, identification of key targets specifically to HCC is an urgent requirement. Herein, an iTRAQ quantitative proteomic approach was employed to identify differentially expressed proteins in HCC tumor tissues. Of the upregulated tumor related proteins, minichromosome maintenance 2 (MCM2), a DNA replication licensing factor was one of the most significantly altered proteins, and its overexpression was confirmed using tissue microarray...
May 11, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29749232/towards-spectral-library-free-maldi-tof-ms-bacterial-identification
#15
Ding Cheng, Liang Qiao, Péter Horvatovich
Bacterial identification is of great importance in clinical diagnosis, environmental monitoring and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interests, and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains...
May 11, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29747501/multi-proteomic-and-transcriptomic-analysis-of-oncogenic-%C3%AE-catenin-molecular-networks
#16
Rob M Ewing, Jing Song, Giridharan Gokulrangan, Sheldon Bai, Emily Bowler, Rachel Bolton, Paul Skipp, Yihua Wang, Zhenghe Wang
Dys-regulation of Wnt signalling is a frequent occurrence in many different cancers. Oncogenic mutations of CTNNB1/β-catenin, the key nuclear effector of canonical Wnt signalling, lead to accumulation and stabilization of β-catenin protein with diverse effects in cancer cells. Although the transcriptional response to Wnt/β-catenin signaling activation has been widely studied, an integrated understanding of the effects of oncogenic β-catenin on molecular networks is lacking. We used Affinity-Purification Mass-Spectrometry (AP-MS), label-free LC-MS/MS and RNA-Seq to compare protein-protein interactions, protein expression and gene-expression in colorectal cancer cells expressing mutant/oncogenic or wild-type β-catenin...
May 10, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29745666/enhanced-quantitative-lc-ms-ms-analysis-of-n-linked-glycans-derived-from-glycoproteins-using-sodium-deoxycholate-detergent
#17
Rui Zhu, Shiyue Zhou, Wenjing Peng, Yifan Huang, Parvin Mirzaei, Kaitlyn Donohoo, Yehia Mechref
Protein glycosylation is a common protein post-translational modification (PTM) in living organisms and has been shown to associate with multiple diseases, and thus may potentially be a biomarker of such diseases. Efficient protein/glycoprotein extraction is a crucial step in the preparation of N-glycans derived from glycoproteins prior to LC-MS analysis. Convenient, efficient and unbiased sample preparation protocols are needed. Herein, we evaluated the use of sodium deoxycholate (SDC) acidic labile detergent to release N-glycans of glycoproteins derived from biological samples such as cancer cell lines...
May 10, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29737853/correction-to-rna-and-protein-interactors-with-tdp-43-in-human-spinal-cord-lysates-in-amyotrophic-lateral-sclerosis
#18
Kathryn Volkening, Brian A Keller, Cheryl Leystra-Lantz, Michael J Strong
No abstract text is available yet for this article.
May 8, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29737851/large-scale-label-free-quantitative-mapping-of-the-sputum-proteome
#19
James P R Schofield, Dominic Burg, Joost Brandsma, Doroteya Staykova, Caterina Folisi, Aruna Bansal, Ben Nicholas, Yang Xian, Anthony Rowe, Julie Corfield, Susan Wilson, Jonathan Ward, Rene Lutter, Louise Fleming, Dominick E Shaw, Per S Bakke, Massimo Caruso, Sven-Erik Dahlén, Stephen J Fowler, Simone Hashimoto, Ildiko Horvath, Peter Howarth, Norbert Krug, Paolo Montuschi, Marek Sanak, Thomas Sandstrom, Florian Singer, Kai Sun, Ioannis Pandis, Charles Auffray, Ana R Sousa, Ian M Adcock, Kian Fan Chung, Peter J Sterk, Ratko Djukanovic, Paul J Skipp
Analysis of induced sputum supernatant is a minimally invasive approach to study the epithelial lining fluid and, thereby, provide insight into normal lung biology and the pathobiology of lung diseases. We present here a novel proteomics approach to sputum analysis developed within the U-BIOPRED (Unbiased BIOmarkers Predictive of REspiratory Disease outcomes) international project. We present practical and analytical techniques to optimise the detection of robust biomarkers in proteomic studies. The normal sputum proteome was derived using data-independent HDMSE applied to 40 healthy non-smoking participants, which provides an essential baseline from which to compare modulation of protein expression in respiratory diseases...
May 8, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29718670/evaluation-of-nci-7-cell-line-panel-as-a-reference-material-for-clinical-proteomics
#20
David J Clark, Yingwei Hu, William Bocik, Lijun Chen, Michael Schnaubelt, Rhonda Roberts, Punit Shah, Gordon Whiteley, Hui Zhang
Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance; however, inherent drawbacks of PDX-derived material, including extended time needed to grow tumors and high level of expertise needed, have resulted in efforts to identify a new source of CompRef material...
May 8, 2018: Journal of Proteome Research
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