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proteomics methods

Vincent Hervé, Harold Duruflé, Hélène San Clemente, Cécile Albenne, Thierry Balliau, Michel Zivy, Christophe Dunand, Elisabeth Jamet
Plant cells are surrounded by cell walls playing many roles during development and in response to environmental constraints. Cell walls are mainly composed of polysaccharides (cellulose, hemicelluloses and pectins), but they also contain proteins which are critical players in cell wall remodelling processes. Today, the cell wall proteome of Arabidopsis thaliana, a major dicot model plant, comprises more than 700 proteins predicted to be secreted (CWPs) identified in different organs or in cell suspension cultures...
October 24, 2016: Proteomics
Paolo Cifani, Alex Kentsis
Given superior analytical features, mass spectrometry proteomics is well suited for the basic investigation and clinical diagnosis of human disease. Modern mass spectrometry enables detailed functional characterization of the pathogenic biochemical processes, as achieved by accurate and comprehensive quantification of proteins and their regulatory chemical modifications. Here, we describe how high-accuracy mass spectrometry in combination with high-resolution chromatographic separations can be leveraged to meet these analytical requirements in a mechanism-focused manner...
October 24, 2016: Proteomics
Hui Liu, Fan Zhang, Shital Kumar Mishra, Shuigeng Zhou, Jie Zheng
Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data...
October 24, 2016: Scientific Reports
Yipeng Du, Zichao Zhai, Ying Li, Ming Lu, Tanxi Cai, Bo Zhou, Lei Huang, Taotao Wei, Tingting Li
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins in low abundance or absent in specific biological samples. To circumvent these problems, we developed a computational method to predict lysine acylation, including acetylation, malonylation, succinylation, and glutarylation. The prediction algorithm integrated flanking primary sequence determinants and evolutionary conservation of acylated lysine, as well as multiple protein functional annotation features including gene ontology, conserved domains and protein-protein interactions...
October 24, 2016: Journal of Proteome Research
Sophie Sabherwal, Jane A English, Melanie Föcking, Gerard Cagney, David R Cotter
Recent evidence supports an association between systemic abnormalities and the pathology of psychotic disorders which has led to the search for peripheral blood-based biomarkers. Areas covered: Here, we summarize blood biomarker findings in schizophrenia from the literature identified by two methods currently driving biomarker discovery in the human proteome; mass spectrometry and multiplex immunoassay. From a total of 14 studies in the serum or plasma of drug-free schizophrenia patients; 47 proteins were found to be significantly altered twice or more, in the same direction...
October 22, 2016: Expert Review of Proteomics
Masayuki Yokoi, Fumio Hanaoka
Mammalian cells express two homologs of yeast Rad23, the so-called homolog of Rad23 (HR23) proteins. The HR23 proteins were identified more than two decades ago as factors involved in initiation of global genome nucleotide excision repair (GG-NER) along with their interacting partner, xeroderma pigmentosum group C (XPC) protein. Because the HR23 genes encode proteins harboring ubiquitin-like (UBL) domains at their N-termini and two ubiquitin-associated (UBA) domains in their central- and C-terminal regions, the link between HR23 proteins and proteolytic degradation has been widely explored by several methods, including yeast two-hybrid screening and co-affinity purification...
October 19, 2016: Gene
Erica T Goddard, Ryan C Hill, Alexander Barrett, Courtney Betts, Qiuchen Guo, Ori Maller, Virginia F Borges, Kirk C Hansen, Pepper Schedin
Normal epithelium exists within a dynamic extracellular matrix (ECM) that is tuned to regulate tissue specific epithelial cell function. As such, ECM contributes to tissue homeostasis, differentiation, and disease, including cancer. Though it is now recognized that the functional unit of normal and transformed epithelium is the epithelial cell and its adjacent ECM, we lack a basic understanding of tissue-specific ECM composition and abundance, as well as how physiologic changes in ECM impact cancer risk and outcomes...
October 19, 2016: International Journal of Biochemistry & Cell Biology
Dinesh K Yadav, Neelam Yadav, Sarika Yadav, Shafiul Haque, Narendra Tuteja
Advancements in peptide fusion technologies to maximize the protein production has taken a big leap to fulfill the demands of post-genomics era targeting elucidation of structure/function of the proteome and its therapeutic applications, by over-expression in heterologous expression systems. Despite being most preferred protein expression system armed with variety of cardinal fusion tags, expression of the functionally active recombinant protein in E. coli remains plagued. The present review critically analyses the aptness of well-characterized fusion tags utilized for over-expression of recombinant proteins with improved solubility and their compatibility with downstream purification procedures...
October 19, 2016: Archives of Biochemistry and Biophysics
Q Chen, X Ke, J S Zhang, S Y Lai, F Fang, W M Mo, Y P Ren
Fraud in milk and dairy products occurs when cow milk is added to sheep and goat milk for economic reasons. No reliable, selective, and sensitive method exists for quantifying the milk percentage of different species. This work reports the development and validation of a proteomics-based method for the qualitative detection and quantitative determination of cow, sheep, and goat milks in the raw materials used for dairy products. β-Lactoglobulin was selected as the protein marker because it is a major protein in milk and whey powder...
October 19, 2016: Journal of Dairy Science
Zhigang Sui, Yejing Weng, Qun Zhao, Nan Deng, Fei Fang, Xudong Zhu, Yichu Shan, Lihua Zhang, Yukui Zhang
The cartilage zone of the velvet antler is richly vascularized, this being a major difference to the classical cartilage, in which there are no blood vessels. Angiogenesis and rapid growth of vasculature in velvet antler cartilage (VAC) make it an ideal model for discovering the novel angiogenic regulatory factors. However, the proteomic analysis of VAC is challenging due to the serious interference of proteoglycans (PGs) and collagens. To achieve a comprehensive proteome characterization of VAC, herein, we developed an ionic liquid-based method using 1-dodecyl-3-methylimidazolium chloride ([C12-mim]Cl) for selective extraction of cellular proteins from VAC...
December 1, 2016: Talanta
Saroj Rajvanshi, Kirti Choudhary, Nirupama Agrawal
The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools...
October 17, 2016: Experimental Parasitology
Simona Arena, Giovanni Renzone, Chiara D'Ambrosio, Anna Maria Salzano, Andrea Scaloni
Heating of milk and dairy products is done using various technological processes with the aim of preserving microbiological safety and extending shelf-life. These treatments result in chemical modifications in milk proteins, mainly generated as a result of the Maillard reaction. Recently, different bottom-up proteomic methods have been applied to characterize the nature of these structural changes and the modified amino acids in model protein systems and/or isolated components from thermally-treated milk samples...
March 15, 2017: Food Chemistry
Daniel V Guebel, Néstor V Torres
Motivation: In the brain of elderly-healthy individuals, the effects of sexual dimorphism and those due to normal aging appear overlapped. Discrimination of these two dimensions would powerfully contribute to a better understanding of the etiology of some neurodegenerative diseases, such as "sporadic" Alzheimer. Methods: Following a system biology approach, top-down and bottom-up strategies were combined. First, public transcriptome data corresponding to the transition from adulthood to the aging stage in normal, human hippocampus were analyzed through an optimized microarray post-processing (Q-GDEMAR method) together with a proper experimental design (full factorial analysis)...
2016: Frontiers in Aging Neuroscience
Xin Ma, Jing Liu, Zhengxiang Zhang, Tao Bo, Yu Bai, Huwei Liu
RATIONALE: Quadrupole based tandem mass spectrometry (MS/MS) plays critical role in "omics" studies. However, when a particular m/z precursor is selected by the quadrupole, ions other than the precursor are not transmitted through, the sensitivity and dynamic range thus diminish. Therefore, separation techniques such as ion mobility (IM) is coupled with MS/MS to improve it. METHODS: In this workflow, every IM-mass spectrometry (MS) scan was followed by one high collision energy (CE) scan...
October 19, 2016: Rapid Communications in Mass Spectrometry: RCM
Ji-Yong An, Zhu-Hong You, Xing Chen, De-Shuang Huang, Guiying Yan, Da-Fu Wang
Self-interacting proteins (SIPs) play an essential role in cellular functions and the evolution of protein interaction networks (PINs). Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a robust and accurate computational approach for SIPs prediction. In this study, we propose a novel computational method for predicting SIPs from protein amino acids sequence. Firstly, a novel feature representation scheme based on Local Binary Pattern (LBP) is developed, in which the evolutionary information, in the form of multiple sequence alignments, is taken into account...
October 19, 2016: Molecular BioSystems
Qian Qi, Guoquan Yan, Chunhui Deng, Xiangmin Zhang
The process of protein digestion is a critical step for successful protein identification in proteomic analysis. Many efforts have been dedicated to enhancing the digestion efficiency for sufficient digestion. Among these approaches, protein complete denaturation with denaturants is a common process for better digestion. However, the removal of denaturants was tedious or would cause protein loss and other problems. In this work, a feasible digestion approach, immobilized protein digestion (IPD), based on covalent binding has been developed...
October 18, 2016: Analytical and Bioanalytical Chemistry
Elena W Y Hsieh, Joseph D Hernandez
PURPOSE OF REVIEW: This review gives an overview of the systems-immunology single-cell proteomic and transcriptomic approaches that can be applied to study primary immunodeficiency. It also introduces recent advances in multiparameter tissue imaging, which allows extensive immune phenotyping in disease-affected tissue. RECENT FINDINGS: Mass cytometry is a variation of flow cytometry that uses rare earth metal isotopes instead of fluorophores as tags bound to antibodies, allowing simultaneous measurement of over 40 parameters per single-cell...
October 5, 2016: Current Opinion in Allergy and Clinical Immunology
Leslie Muller, Luc Fornecker, Alain Dorsselaer, Sarah Cianférani, Christine Carapito
Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide-gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD)...
October 17, 2016: Proteomics
Igor S Bryukhovetskiy, Inessa V Dyuizen, Valeriy E Shevchenko, Andrey S Bryukhovetskiy, Polina V Mischenko, Elena V Milkina, Yuri S Khotimchenko
Glioblastoma multiforme is an aggressive malignant brain tumor with terminal consequences. A primary reason for its resistance to treatment is associated with cancer stem cells (CSCs), of which there are currently no effective ways to destroy. It remains unclear what cancer cells become a target of stem cell migration, what the role of this process is in oncogenesis and what stem cell lines should be used in developing antitumor technologies. Using modern post‑genome technologies, the present study investigated the migration of human stem cells to cancer cells in vitro, the comparative study of cell proteomes of certain stem cells (including CSCs) was conducted and stem cell migration in vivo was examined...
October 13, 2016: Molecular Medicine Reports
Fengchao Yu, Ning Li, Weichuan Yu
In computational proteomics, identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process...
October 17, 2016: Journal of Proteome Research
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