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proteomics analysis tools

Xudong Zhu, Ju Chu, Yonghong Wang
The field of microbiology has traditionally been concerned with and focused on studies at the population level. Microfluidic platforms have emerged as important tools for biology research at a small scale, even down to a single cell level. The spatial and temporal control of cells and stimuli transported by microfluidic channels in well-designed microsystems realized the studies of specific cells in a controlled microenvironment. The true cellular physiology responses, which were obtained mostly by inference from population-level data, could be revealed in this way...
December 8, 2017: Biotechnology Journal
Maria Rita Sciuto, Uwe Warnken, Martina Schnölzer, Cecilia Valvo, Lidia Brunetto, Alessandra Boe, Mauro Biffoni, Peter H Krammer, Ruggero De Maria, Tobias Longin Haas
Co-immunoprecipitation (co-IP) is one of the most frequently used techniques to study protein-protein (PPIs) or protein-nucleic acid interactions (PNIs). However, the presence of co-precipitated contaminants is a well-recognized issue associated with single-step co-IPs. To overcome this limitation, we developed the two-step co-IP (TIP) strategy that enables sequential co-immunoprecipitations of endogenous protein complexes. TIP can be performed with a broad range of mono- and polyclonal antibodies targeting a single protein or different components of a given complex...
December 7, 2017: Molecular & Cellular Proteomics: MCP
Charanjit Sandhu, Alia Qureshi, Andrew Emili
Medicine is poised to undergo a digital transformation. High-throughput platforms are creating terabytes of genomic, transcriptomic, proteomic, and metabolomic data. The challenge is to interpret these data in a meaningful manner - to uncover relationships that are not readily apparent between molecular profiles and states of health or disease. This will require the development of novel data pipelines and computational tools. The combined analysis of multi-dimensional data is referred to as 'panomics'. The ultimate hope of integrative panomics is that it will lead to the discovery and application of novel markers and targeted therapeutics that drive forward a new era of 'precision medicine' where inter-individual variation is accounted for in the treatment of patients...
December 4, 2017: Trends in Molecular Medicine
Thilo Muth, Fabian Kohrs, Robert Heyer, Dirk Benndorf, Erdmann Rapp, Udo Reichl, Lennart Martens, Bernhard Y Renard
Metaproteomics, the mass spectrometry-based analysis of proteins from multi-species samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce the MetaProteomeAnalyzer (MPA) Portable software. In contrast to the original server-based MPA application, this newly developed tool no longer requires computational expertise for installation, and is now independent of any relational database system. In addition, MPA Portable now supports state-of-the-art database search engines and a convenient command line interface for high-performance data processing tasks...
December 7, 2017: Analytical Chemistry
Marie-Caroline Smith, Emma Timmins-Schiffman, Monika Coton, Emmanuel Coton, Nolwenn Hymery, Brook L Nunn, Stéphanie Madec
Numerous surveys have highlighted the natural co-occurrence of deoxynivalenol (DON) and zearalenone (ZEA) mycotoxins in food and feed. Nevertheless, data regarding cellular mechanisms involved in response to their individual and simultaneous exposures are lacking. In this study, in order to analyze how low mycotoxin doses could impact cellular physiology and homeostasis, proteomic profiles of proliferating human hepatocytes (HepaRG) exposed for 1h and 24h to low DON and ZEA cytotoxicity levels (0.2 and 20μM respectively), alone or in combination, were analyzed by LC-MS/MS...
December 2, 2017: Journal of Proteomics
Abhigya Mookherjee, Miklos Guttman
Over the past two decades mass spectrometry (MS) has enabled high throughput studies on the level of a complex proteome. While it has similarly advanced glycobiology, the level of progress has been more restrained. This is in large part due to the diversity and complexity of carbohydrate structures. While MS is now routinely used for glycobiology, it suffers from a critical limitation, that is the inability to resolve isobaric structures. Since so many structurally and functionally distinct carbohydrates are indistinguishable by MS, additional techniques are needed for detailed structural analysis...
December 1, 2017: Current Opinion in Chemical Biology
Kai Cheng, Zhibin Ning, Xu Zhang, Leyuan Li, Bo Liao, Janice Mayne, Alain Stintzi, Daniel Figeys
BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of microbial ecosystems. Currently, metaproteomics provide qualitative and quantitative information of proteins, providing insights into the functional changes of microbial communities. However, computational analysis of large-scale data generated in metaproteomic studies remains a challenge...
December 2, 2017: Microbiome
Marimu Sakumoto, Rieko Oyama, Mami Takahashi, Yoko Takai, Fusako Kito, Kumiko Shiozawa, Zhiwei Qiao, Makoto Endo, Akihiko Yoshida, Akira Kawai, Tadashi Kondo
Clear cell sarcoma (CCS) is an aggressive mesenchymal malignancy characterized by the unique chimeric EWS-ATF1 fusion gene. Patient-derived cancer models are essential tools for the understanding of tumorigenesis and the development of anti-cancer drugs; however, only a limited number of CCS cell lines exist. The objective of this study was to establish patient-derived CCS models. We established patient-derived CCS models from a 43-yr-old female patient. We prepared the patient-derived xenografts (PDXs) from tumor tissues obtained through biopsy or surgery and isolated stable cell lines from PDXs and the original tumor tissue...
December 1, 2017: In Vitro Cellular & Developmental Biology. Animal
Chengmei Xie, Hongyan Shen, Hui Zhang, Jinting Yan, Yang Liu, Fuwen Yao, Xi Wang, Zhongyi Cheng, Tie-Shan Tang, Caixia Guo
Environmental stresses are important factors causing male infertility which attracts broad attention. Protein acetylation is a pivotal post-translational modification and modulates diverse physiological processes including spermatogenesis. In this study, we employed quantitative proteomic techniques and bioinformatics tools to analyze the alterations of acetylome profile of mouse testis after heat shock and X-irradiation. Overall, we identified 1139 lysine acetylation sites in 587 proteins in which 1020 lysine acetylation sites were quantified...
November 28, 2017: Biochimica et Biophysica Acta
Jonathon O'Brien, Jeremy D O'Connell, Joao A Paulo, Sanjukta Thakurta, Christopher M Rose, Michael P Weekes, Edward L Huttlin, Steven P Gygi
Mass spectrometry (MS) has become an accessible tool for whole proteome quantitation with the ability to characterize protein expression across thousands of proteins within a single experiment. A subset of MS quantification methods (e.g., SILAC and label-free) monitor the relative intensity of intact peptides, where thousands of measurements can be made from a single mass spectrum. An alternative approach, isobaric labeling, enables precise quantification of multiple samples simultaneously through unique and sample specific mass reporter ions...
December 1, 2017: Journal of Proteome Research
Roshanak Aslebagh, Devika Channaveerappa, Kathleen F Arcaro, Costel C Darie
Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk...
November 29, 2017: Electrophoresis
Balkis Eddhif, Justin Lange, Nadia Guignard, Yann Batonneau, Jonathan Clarhaut, Sébastien Papot, Claude Geffroy-Rodier, Pauline Poinot
Sample preparation for mass spectrometry-based proteomics is a key step for ensuring reliable data. In gel-free experimental workflows, protein purification often starts with a precipitation stage using trichloroacetic acid (TCA). In presence of TCA, proteins precipitate in a stable molten globule state making the pellet difficult to solubilize in aqueous buffer for proteolytic digestion and MS analysis. In this context, the objective of this work was to study the suitability of a novel agent, ethanol/HCl, for the washing of TCA-precipitated proteins...
November 27, 2017: Journal of Proteomics
Chalermchai Somboonpatarakun, Rutchanee Rodpai, Pewpan M Intapan, Oranuch Sanpool, Lakkhana Sadaow, Chaisiri Wongkham, Tonkla Insawang, Thidarut Boonmars, Wanchai Maleewong
The present study explored potentially immunogenic proteins of the encapsulated (Trichinella spiralis) and non-encapsulated (T. pseudospiralis, T. papuae) species within the genus Trichinella. The somatic muscle larval extracts of each species were subjected to immunoblotting analysis using human T. spiralis-infected serum samples. Fifteen reactive bands of all three species were selected for further protein identification by liquid chromatography-tandem mass spectrometry, and their possible functions were ascertained using the gene ontology...
November 30, 2017: Parasitology Research
Jordi Vilaplana, Rui Alves, Francesc Solsona, Jordi Mateo, Ivan Teixidó, Marc Pifarré
MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the processes of interest and their function. The main goal of this work was to identify the areas where the performance of the MetReS database performance could be improved and to test whether this improvement would scale to larger datasets and more complex types of analysis...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Doudou Zhang, Dandan Lan, Xiaomin Pang, Beijiao Cui, Ligai Bai, Haiyan Liu, Hongyuan Yan
A double-functionalized polymer monolithic column was fabricated within the confines of a stainless-steel column (50 mm × 4.6 mm i.d.) via a facile method using iron porphyrin, ionic liquid (1-allyl-3-methylimidazolium chloride) and 1,10-decanediol dimethacrylate as tri-monomers; ethylene dimethacrylate as a crosslinker; polyethylene glycol 400 and N,N-dimethylformamide as co-porogens; benzoyl peroxide and N,N-dimethyl aniline as the redox initiation system. Results obtained from scanning electron microscopy, nitrogen adsorption-desorption, and mercury intrusion porosimetry confirmed the uniform pore structure and the pore size distribution of macro-pores...
November 29, 2017: Analyst
Sabryna Junker, Sandra Maaß, Andreas Otto, Stephan Michalik, Friedrich Morgenroth, Ulf Gerth, Michael Hecker, Dörte Becher
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus. Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence...
November 28, 2017: Molecular & Cellular Proteomics: MCP
A Corigliano, M Preianò, R Terracciano, R Savino, M De Gori, O Galasso, G Gasparini
An attractive method for osteoarthritis (OA) staging is the measurement of biochemical markers in biological fluids, which could reflect dynamic and quantitative changes in joint remodeling and therefore disease progression. Proteome analysis has been recognized as one of the most effective tools to explore biomarkers as it can furnish a wealth of information in both diagnosis and prognosis of diseases. We have recently described an innovative tool for peptidome and lipidome profiling of fluids based on mesoporous aluminosilicate (MPAS) and Matrix-Assisted Laser Desorption/Ionization time-of-flight Mass Spectrometry (MALDI-TOF MS)...
October 2017: Journal of Biological Regulators and Homeostatic Agents
Syed Kashif Raza, Mahwish Saleem, Tahir Shamsi, M Iqbal Choudhary, Atta-Ur-Rahman, Syed Ghulam Musharraf
Acute myeloid leukaemia (AML) is a type of cancer affecting all ages but it is more common in adults, as compared to children. Recent advancements in proteomics and mass spectrometry tools, offer a comprehensive solution to study the molecular complexity of diseases, such as cancers. This study is focused on the proteomic profiling of AML in comparison to healthy control for which, a systematic 5D proteomic approach for the fractionation of pooled plasma samples was used. Methodology includes depletion of Top-7 abundant proteins, ZOOM-isoelectric focusing (ZOOM-IEF), two-dimensional gel electrophoresis (2-DGE), and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis followed by the validation of identified biomarker proteins using enzyme linked immunosorbent assay (ELISA)...
November 27, 2017: Scientific Reports
Reaz Uddin, Quratulain Nehal Siddiqui, Syed Sikander Azam, Bibi Saima, Abdul Wadood
Among the resistant isolates of tuberculosis (TB), the multidrug resistance tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB) are the areas of growing concern for which the front-line antibiotics are no more effective. As a result, the search of new therapeutic targets against TB is an imperative need of time. On the other hand, the target identification is an a priori step in drug discovery based research. Furthermore, the availability of the complete proteomic data of extensively drug resistant Mycobacterium tuberculosis (XDR-MTB) made it possible to carry out in silico analysis for the discovery of new drug targets...
November 22, 2017: European Journal of Pharmaceutical Sciences
Hui-Yin Chang, Ching-Tai Chen, Chu-Ling Ko, Yi-Ju Chen, Yu-Ju Chen, Wen-Lian Hsu, Chiun-Gung Juo, Ting-Yi Sung
Top-down proteomics using liquid chromatogram coupled with mass spectrometry has been increasingly applied for analyzing intact proteins to study genetic variation, alternative splicing, and post-translational modifications (PTMs) of the proteins (proteoforms). However, only a few tools have been developed for charge state deconvolution, monoisotopic/average molecular weight determination and quantitation of proteoforms from LC-MS1 spectra. Though Decon2LS and MASH Suite Pro have been available to provide intra-spectrum charge state deconvolution and quantitation, manual processing is still required to quantify proteoforms across multiple MS1 spectra...
November 22, 2017: Analytical Chemistry
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