Articles

Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolution...

Authors: Raghuveera Kumar Goel, Mona Meyer, Marta Paczkowska, Jüri Reimand, Frederick Vizeacoumar, Franco Vizeacoumar, TuKiet T. Lam and Kiven Erique Lukong

Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium

The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cel...

Authors: Lancia N. F. Darville and Bernd H. A. Sokolowski

Comparative iTRAQ proteomics revealed proteins associated with horn development in yak

The practice of dehorning yak raises animal safety concerns, which have been addressed by selective breeding to obtain genetically hornless yak. The POLLED locus in yak has been studied extensively; however, l...

Authors: Mingna Li, Xiaoyun Wu, Xian Guo, Pengjia Bao, Xuezhi Ding, Min Chu, Chunnian Liang and Ping Yan

Correction to: Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

Following publication of the original article [1]

Authors: Christos Spanos, Elaina M. Maldonado, Ciarán P. Fisher, Petchpailin Leenutaphong, Ernesto Oviedo-Orta, David Windridge, Francisco J. Salguero, Alexandra Bermúdez-Fajardo, Mark E. Weeks, Caroline Evans, Bernard M. Corfe, Naila Rabbani, Paul J. Thornalley, Michael H. Miller, Huan Wang, John F. Dillon…

iTRAQ-Based Proteomic Analysis reveals possible target-related proteins and signal networks in human osteoblasts overexpressing FGFR2

Fibroblast growth factor receptor 2 (FGFR2) play a vital role in skeletogenesis. However, the molecular mechanisms triggered by FGFR2 in osteoblasts are still not fully understood. In this study, proteomics an...

Authors: Tianyi Cai, Baojin Wu, Xinjie Tang, Zhaoping Zhou, Junyi Yang, Ronghu Ke and Xiongzheng Mu

In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix

The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of t...

Authors: Karlheinz Mann, Nicolas Cerveau, Meike Gummich, Monika Fritz, Matthias Mann and Daniel J. Jackson

Correction to: Proteomic characterization of adrenal gland embryonic development reveals early initiation of steroid metabolism and reduction of the retinoic acid pathway

Upon publication of the original article [1], Marwa Eltoweissy noticed that her affiliation: “3. Department of Zoology, Faculty of Science, Alexandria University, Alexandria, Egypt” was missing. This affiliati...

Authors: Gry H. Dihazi, Gerhard A. Mueller, Abdul R. Asif, Marwa Eltoweissy, Johannes T. Wessels and Hassan Dihazi

Proteomic analysis of buccal gland secretion from fasting and feeding lampreys (Lampetra morii)

Previous studies have shown that lamprey buccal glands contain some regulators related to anticoagulation, nociception, and immune responses due to the blood sucking habit. Regrettably, the protein expression ...

Authors: Bowen Li, Meng Gou, Jianmei Han, Xiaofei Yuan, Yingying Li, Tiesong Li, Qi Jiang, Rong Xiao and Qingwei Li

ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity

Euphorbia lathyris L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of E...

Authors: Yu Zhang, Yingzi Wang, Shaojing Li, Xiuting Zhang, Wenhua Li, Shengxiu Luo, Zhenyang Sun and Ruijie Nie

In vitro gentamicin exposure alters caveolae protein profile in cochlear spiral ligament pericytes

The aminoglycoside antibiotic gentamicin is an ototoxic drug and has been used experimentally to investigate cochlear damage induced by noise.

Authors: Elisa Ghelfi, Yohann Grondin, Emil J. Millet, Adam Bartos, Magda Bortoni, Clara Oliveira Gomes dos Santos, Humberto J. Trevino-Villarreal, Rosalinda Sepulveda and Rick Rogers

Effects of the complete replacement of fish oil with linseed oil on growth, fatty acid composition, and protein expression in the Chinese mitten crab (Eriocheir sinensis)

The finite marine resources make it difficult for us to obtain enough fish oil (FO) used in aquatic feeds. Another sustainable ingredients should be found to substitute FO. The effects of replacing FO with veg...

Authors: Banghong Wei, Zhigang Yang, Yongxu Cheng, Jianyi Wang and Junyu Zhou

Profiling the interactome of protein kinase C ζ by proteomics and bioinformatics

Protein kinase C ζ (PKCζ), an isoform of the atypical protein kinase C, is a pivotal regulator in cancer. However, the molecular and cellular mechanisms whereby PKCζ regulates tumorigenesis and metastasis are ...

Authors: Chunyu Hou, Yuan Li, Huiqin Liu, Mengjiao Dang, Guoxuan Qin, Ning Zhang and Ruibing Chen

Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. However, its molecular pathogenesis is incompletely characterized and clinical biomarkers remain scarce. The aims of these ...

Authors: Christos Spanos, Elaina M. Maldonado, Ciarán P. Fisher, Petchpailin Leenutaphong, Ernesto Oviedo-Orta, David Windridge, Francisco J. Salguero, Alexandra Bermúdez-Fajardo, Mark E. Weeks, Caroline Evans, Bernard M. Corfe, Naila Rabbani, Paul J. Thornalley, Michael H. Miller, Huan Wang, John F. Dillon…

Effect of ovarian cancer ascites on SKOV-3 cells proteome: new proteins associated with aggressive phenotype in epithelial ovarian cancer

Epithelial ovarian cancer is the second most lethal gynecological cancer worldwide. Ascites can be found in all clinical stages, however in advanced disease stages IIIC and IV it is more frequent and could be ...

Authors: Alfredo Toledo-Leyva, Julio César Villegas-Pineda, Sergio Encarnación-Guevara, Dolores Gallardo-Rincón and Patricia Talamás-Rohana

Proteomic identification of moesin upon exposure to acrolein

Acrolein (allyl Aldehyde) as one of smoke irritant exacerbates chronic airway diseases and increased in sputum of patients with asthma and chronic obstructive lung disease. But underlying mechanism remains unr...

Authors: Pureun-Haneul Lee, Byeong-Gon Kim, Sun-Hye Lee, George D. Leikauf and An-Soo Jang

Chemical proteomics, an integrated research engine for exploring drug-target-phenotype interactions

Authors: Ho Jeong Kwon and Peter Karuso

Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae

Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand ho...

Authors: Yeonyee Oh, Suzanne L. Robertson, Jennifer Parker, David C. Muddiman and Ralph A. Dean

Proteomic analysis of early salt stress responsive proteins in alfalfa roots and shoots

Alfalfa (Medicago sativa) is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue v...

Authors: Junbo Xiong, Yan Sun, Qingchuan Yang, Hong Tian, Heshan Zhang, Yang Liu and Mingxin Chen

Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes

Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no corre...

Authors: Carmine Mancone, Alessio Grimaldi, Giulia Refolo, Isabella Abbate, Gabriella Rozera, Dario Benelli, Gian Maria Fimia, Vincenzo Barnaba, Marco Tripodi, Mauro Piacentini and Fabiola Ciccosanti

Examining the influence of specificity ligands and ATP-competitive ligands on the overall effectiveness of bivalent kinase inhibitors

Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors...

Authors: Margaret L. Wong, Jason Murphy, Edmund Harrington, Carrie M. Gower, Rishi K. Jain, Markus Schirle and Jason R. Thomas

Daptomycin, a last-resort antibiotic, binds ribosomal protein S19 in humans

Daptomycin is a recently introduced, last-resort antibiotic that displays a unique mode of action against Gram-positive bacteria that is not fully understood. Several bacterial targets have been proposed but n...

Authors: Michael P. Gotsbacher, Sungmin Cho, Ho Jeong Kwon and Peter Karuso

Tetrazine ligation for chemical proteomics

Determining small molecule—target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class m...

Authors: Kyungtae Kang, Jongmin Park and Eunha Kim

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific protei...

Authors: Dhiraj P. Murale, Seong Cheol Hong, Md. Mamunul Haque and Jun-Seok Lee

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

In recent years, phenotypic-based screens have become increasingly popular in drug discovery. A major challenge of this approach is that it does not provide information about the mechanism of action of the hit...

Authors: André Mateus, Tomi A. Määttä and Mikhail M. Savitski

The hepatocyte proteome in organotypic rat liver models and the influence of the local microenvironment

Liver models that closely mimic the in vivo microenvironment are useful for understanding liver functions, capabilities, and intercellular communication processes. Three-dimensional (3D) liver models assembled...

Authors: Lucas T. Vu, Sophia M. Orbach, W. Keith Ray, Margaret E. Cassin, Padmavathy Rajagopalan and Richard F. Helm

Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum

Unlike humans, there is currently no publicly available reference mass spectrometry-based circulating acellular proteome data for sheep, limiting the analysis and interpretation of a range of physiological cha...

Authors: Saul Chemonges, Rajesh Gupta, Paul C. Mills, Steven R. Kopp and Pawel Sadowski

The effect of microbial challenge on the intestinal proteome of broiler chickens

In poultry production intestinal health and function is paramount to achieving efficient feed utilisation and growth. Uncovering the localised molecular mechanisms that occur during the early and important per...

Authors: Emily L. O’Reilly, Richard J. Burchmore, Nicholas H. Sparks and P. David Eckersall

Water deficit mechanisms in perennial shrubs Cerasus humilis leaves revealed by physiological and proteomic analyses

Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry (Cerasus humilis) is a good perennial plant for studying the physiological and...

Authors: Zepeng Yin, Jing Ren, Lijuan Zhou, Lina Sun, Jiewan Wang, Yulong Liu and Xingshun Song

Merging clinical chemistry biomarker data with a COPD database - building a clinical infrastructure for proteomic studies

Data from biological samples and medical evaluations plays an essential part in clinical decision making. This data is equally important in clinical studies and it is critical to have an infrastructure that en...

Authors: Jonatan Eriksson, Simone Andersson, Roger Appelqvist, Elisabet Wieslander, Mikael Truedsson, May Bugge, Johan Malm, Magnus Dahlbäck, Bo Andersson, Thomas E. Fehniger and György Marko-Varga

Proteomic profiling of HBV infected liver biopsies with different fibrotic stages

Hepatitis B virus (HBV) is a global health problem, and infected patients if left untreated may develop cirrhosis and eventually hepatocellular carcinoma. This study aims to enlighten pathways associated with ...

Authors: Seyma Katrinli, Kamil Ozdil, Abdurrahman Sahin, Oguzhan Ozturk, Gozde Kir, Ahmet Tarik Baykal, Emel Akgun, Omer Sinan Sarac, Mehmet Sokmen, H. Levent Doğanay and Gizem Dinler Doğanay

Disulfide proteomics of rice cultured cells in response to OsRacl and probenazole-related immune signaling pathway in rice

Reactive oxygen species (ROS) production is an early event in the immune response of plants. ROS production affects the redox-based modification of cysteine residues in redox proteins, which contribute to prot...

Authors: Kazuko Morino, Mayumi Kimizu and Masayuki Fujiwara

Proteomic analysis of microparticles isolated from malaria positive blood samples

Malaria continues to be a great public health concern due to the significant mortality and morbidity associated with the disease especially in developing countries. Microparticles (MPs), also called plasma mem...

Authors: Samuel Antwi-Baffour, Jonathan Kofi Adjei, Francis Agyemang-Yeboah, Max Annani-Akollor, Ransford Kyeremeh, George Awuku Asare and Ben Gyan

Protein profiles of hatchery egg shell membrane

Eggshells which consist largely of calcareous outer shell and shell membranes, constitute a significant part of poultry hatchery waste. The shell membranes (ESM) not only contain proteins that originate from e...

Authors: N. C. Rath, R. Liyanage, S. K. Makkar and J. O. Lay Jr.

Proteome changes in the small intestinal mucosa of growing pigs with dietary supplementation of non-starch polysaccharide enzymes

Non-starch polysaccharide enzymes (NSPEs) have long been used in monogastric animal feed production to degrade non-starch polysaccharides (NSPs) to oligosaccharides in order to promote growth performance and g...

Authors: Jize Zhang, Yang Gao, Qingping Lu, Renna Sa and Hongfu Zhang

Overgrazing induces alterations in the hepatic proteome of sheep (Ovis aries): an iTRAQ-based quantitative proteomic analysis

The degradation of the steppe of Inner Mongolia, due to overgrazing, has resulted in ecosystem damage as well as extensive reductions in sheep production. The growth performance of sheep is greatly reduced bec...

Authors: Weibo Ren, Xiangyang Hou, Yuqing Wang, Warwick Badgery, Xiliang Li, Yong Ding, Huiqin Guo, Zinian Wu, Ningning Hu, Lingqi Kong, Chun Chang, Chao Jiang and Jize Zhang

An interactomics overview of the human and bovine milk proteome over lactation

Milk is the most important food for growth and development of the neonate, because of its nutrient composition and presence of many bioactive proteins. Differences between human and bovine milk in low abundant...

Authors: Lina Zhang, Aalt D. J. van Dijk and Kasper Hettinga

Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm

Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biom...

Authors: Tyman E. Stanford, Christopher J. Bagley and Patty J. Solomon

Proteomic based approach for characterizing 4-hydroxy-2-nonenal induced oxidation of buffalo (Bubalus bubalis) and goat (Capra hircus) meat myoglobins

Myoglobin (Mb) is a sarcoplasmic heme protein primarily responsible for meat color and its chemistry is species specific. 4-hydroxy-2-nonenal (HNE) is a cytotoxic lipid derived aldehyde detected in meat and wa...

Authors: Naveena B. Maheswarappa, K. Usha Rani, Y. Praveen Kumar, Vinayak V. Kulkarni and Srikanth Rapole

Follicular fluid biomarkers for human in vitro fertilization outcome: Proof of principle

Human follicular fluid (FF) is a unique biological fluid in which the oocyte develops in vivo, and presents an optimal source for non-invasive biochemical predictors. Oocyte quality directly influences the emb...

Authors: Fang Chen, Carl Spiessens, Thomas D’Hooghe, Karen Peeraer and Sebastien Carpentier

iTRAQ-based proteomic analysis of myofibrillar contents and relevant synthesis and proteolytic proteins in soleus muscle of hibernating Daurian ground squirrels (Spermophilus dauricus)

Daurian ground squirrels (Spermophilus dauricus) deviate from significant increase of protein catabolism and loss of myofibrillar contents during long period of hibernation inactivity.

Authors: Hui Chang, Shan-Feng Jiang, Kai Dang, Hui-Ping Wang, Shen-Hui Xu and Yun-Fang Gao

Multi-omics analysis on the pathogenicity of Enterobacter cloacae ENHKU01 isolated from sewage outfalls along the Ningbo coastline

The acquisition of iron is important for the pathogenicity of bacteria and blood. Three different culture environments (Fe stimulation, blood agar plate and normal plate) were used to stimulate Enterobacter cloac...

Authors: Dijun Zhang, Weina He, Qianqian Tong, Jun Zhou and Xiurong Su

Proteome profiling reveals insights into cold-tolerant growth in sea buckthorn

Low temperature is one of the crucial environmental factors limiting the productivity and distribution of plants. Sea buckthorn (Hippophae rhamnoides L.), a well recognized multipurpose plant species, live succes...

Authors: Caiyun He, Guori Gao, Jianguo Zhang, Aiguo Duan and Hongmei Luo

Identifying EGFR mutation-induced drug resistance based on alpha shape model analysis of the dynamics

Epidermal growth factor receptor (EGFR) mutation-induced drug resistance is a difficult problem in lung cancer treatment. Studying the molecular mechanisms of drug resistance can help to develop corresponding ...

Authors: Lichun Ma, Bin Zou and Hong Yan

Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process

Plenty of proteomic studies were performed to characterize the allotetraploid upland cotton fiber elongation process, whereas little is known about the elongating diploid cotton fiber proteome.

Authors: Bing Zhang, Shao-Jun Du, Jue Hu, Di Miao and Jin-Yuan Liu

Removal of SDS from biological protein digests for proteomic analysis by mass spectrometry

Metal-organic frameworks (MOFs - MIL-101) are the most exciting, high profiled developments in nanotechnology in the last ten years, and it attracted considerable attention owing to their uniform nanoporosity,...

Authors: Soundharrajan Ilavenil, Naif Abdullah Al-Dhabi, Srisesharam Srigopalram, Young Ock Kim, Paul Agastian, Rajasekhar Baaru, Ki Choon Choi, Mariadhas Valan Arasu, Chun Geon Park and Kyung Hun Park

Differential proteins among normal cervix cells and cervical cancer cells with HPV-16 infection, through mass spectrometry-based Proteomics (2D-DIGE) in women from Southern México

Cervical cancer (CC) is the fourth most common cancer in women worldwide with an estimated 528,000 new cases in 2012. The same year México had an incidence of 13,960 and a mortality of 4769 cases. There are se...

Authors: Idanya Serafín-Higuera, Olga Lilia Garibay-Cerdenares, Berenice Illades-Aguiar, Eugenia Flores-Alfaro, Marco Antonio Jiménez-López, Pavel Sierra-Martínez and Luz del Carmen Alarcón-Romero

Comparative proteome analysis of abdominal adipose tissues between fat and lean broilers

The molecular mechanism underlying broiler fat deposition is still poorly understood.

Authors: Chun-Yan Wu, Yuan-Yuan Wu, Chun-Dong Liu, Yu-Xiang Wang, Wei Na, Ning Wang and Hui Li

Investigation of proteome changes in osteoclastogenesis in low serum culture system using quantitative proteomics

RAW 264.7 cells can differentiate into osteoclasts when cultured in medium supplemented with 1 % FBS. However, the proteomic changes in the development of RAW 264.7 cells into osteoclasts in low serum culture ...

Authors: Qi Xiong, Lihai Zhang, Shaohua Zhan, Wei Ge and Peifu Tang

The association of plasma cystatin C proteoforms with diabetic chronic kidney disease

Cystatin C (CysC) is an endogenous cysteine protease inhibitor that can be used to assess the progression of kidney function. Recent studies demonstrate that CysC is a more specific indicator of glomerular fil...

Authors: Hussein N. Yassine, Olgica Trenchevska, Zhiwei Dong, Yara Bashawri, Juraj Koska, Peter D. Reaven, Randall W. Nelson and Dobrin Nedelkov

Stathmin involvement in the maternal embryonic leucine zipper kinase pathway in glioblastoma

Maternal Embryonic Leucine Zipper Kinase (MELK) is a serine/threonine kinase involved in cell cycle, differentiation, proliferation, and apoptosis. These multiple features are consistent with it being a potent...

Authors: Suely Kazue Nagahashi Marie, Sueli Mieko Oba-Shinjo, Roseli da Silva, Marcela Gimenez, Gisele Nunes Reis, Jean-Pierre Tassan, Jose Cesar Rosa and Miyuki Uno